https://wiki.flybase.org/mediawiki/api.php?action=feedcontributions&user=Arzu+Ozturk+Colak&feedformat=atomFlyBase Wiki - User contributions [en]2024-03-29T10:10:25ZUser contributionsMediaWiki 1.35.3https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172897FlyBase:FAQ2024-02-22T11:04:03Z<p>Arzu Ozturk Colak: </p>
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! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
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! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
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! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
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|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
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! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
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! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
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|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
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! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
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! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
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|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
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! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
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|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
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! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
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|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
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! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
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|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
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! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
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|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
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! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
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|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
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! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
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|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
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! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
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|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
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! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
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|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
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! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
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|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
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! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
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|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
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! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
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! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
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|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
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! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
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|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
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! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
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! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
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|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
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! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
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! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
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|style="text-align: left"| || No, the FlyBase people database was retired.<br />
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! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
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! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
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|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
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! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
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|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
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It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
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! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
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! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
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|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
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! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
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|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
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You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
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The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
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! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
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|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
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! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
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|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
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! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
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! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
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|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
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! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
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|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
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! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
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|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
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! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
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|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
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! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
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|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
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! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
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|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
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! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
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|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
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! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
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|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
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! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
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|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
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! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
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|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
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! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
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|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
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! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
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|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
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! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
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|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
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! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
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|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
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''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
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The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
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! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
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|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
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! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
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|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
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For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
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If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
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If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
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! style="text-align: left" | 9.17. !! style="text-align: left" | Where can I find FlyBase data for older genome assemblies?<br />
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|style="text-align: left"| || FlyBase archives the annotation files (FASTA, GFF, GTF) generated for every release on our [https://ftp.flybase.net/releases/ FlyBase FTP site]; one can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
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The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
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So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
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! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Data from older releases<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data". [https://wiki.flybase.org/wiki/FlyBase:Using_FTP_Archives Using FTP Archives Wiki Page] aims to help users become more familiar with FTP files, so they can figure out how to recapitulate searches done on the full website.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
<br />
===9.17. Where can I find FlyBase data for older genome assemblies?===<br />
FlyBase archives the annotation files generated for every release on our [https://ftp.flybase.net/ FlyBase FTP site]. This includes FASTA and GFF for almost all past releases, and GTF files for Release 6 (dm6) releases. One can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Data from older releases</big>''' ==<br />
===19.1. How do I access data from an older release? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data". [https://wiki.flybase.org/wiki/FlyBase:Using_FTP_Archives Using FTP Archives Wiki Page] aims to help users become more familiar with FTP files, so they can figure out how to recapitulate searches done on the full website.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172896FlyBase:FAQ2024-02-22T11:01:17Z<p>Arzu Ozturk Colak: /* 19. Web server */</p>
<hr />
<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|-<br />
! style="text-align: left" | 9.17. !! style="text-align: left" | Where can I find FlyBase data for older genome assemblies?<br />
|-<br />
|style="text-align: left"| || FlyBase archives the annotation files (FASTA, GFF, GTF) generated for every release on our [https://ftp.flybase.net/releases/ FlyBase FTP site]; one can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
<br />
===9.17. Where can I find FlyBase data for older genome assemblies?===<br />
FlyBase archives the annotation files generated for every release on our [https://ftp.flybase.net/ FlyBase FTP site]. This includes FASTA and GFF for almost all past releases, and GTF files for Release 6 (dm6) releases. One can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Data from older releases</big>''' ==<br />
===19.1. How do I access data from an older release? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data". Using FTP Archives wiki page aims to help users become more familiar with these files, so they can figure out how to recapitulate searches done on the full website.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172895FlyBase:FAQ2024-02-22T09:59:41Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|-<br />
! style="text-align: left" | 9.17. !! style="text-align: left" | Where can I find FlyBase data for older genome assemblies?<br />
|-<br />
|style="text-align: left"| || FlyBase archives the annotation files (FASTA, GFF, GTF) generated for every release on our [https://ftp.flybase.net/releases/ FlyBase FTP site]; one can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
<br />
===9.17. Where can I find FlyBase data for older genome assemblies?===<br />
FlyBase archives the annotation files generated for every release on our [https://ftp.flybase.net/ FlyBase FTP site]. This includes FASTA and GFF for almost all past releases, and GTF files for Release 6 (dm6) releases. One can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172894FlyBase:FAQ2024-02-22T09:59:05Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|-<br />
! style="text-align: left" | 9.17. !! style="text-align: left" | Where can I find FlyBase data for older genome assemblies?<br />
|-<br />
|style="text-align: left"| || FlyBase archives the annotation files (FASTA, GFF, GTF) generated for every release on our [https://ftp.flybase.net/releases/ FlyBase FTP site]; one can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
<br />
===9.17. Where can I find FlyBase data for older genome assemblies?===<br />
FlyBase archives the annotation files generated for every release on our [https://ftp.flybase.net/ FlyBase FTP site]. This includes FASTA and GFF for almost all past releases, and GTF files for Release 6 (dm6) releases. One can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172893FlyBase:FAQ2024-02-22T09:54:04Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|-<br />
! style="text-align: left" | 9.17. !! style="text-align: left" | Where can I find FlyBase data for older genome assemblies?<br />
|-<br />
|style="text-align: left"| || FlyBase archives the annotation files (FASTA, GFF, GTF) generated for every release on our [https://ftp.flybase.net/releases/ FlyBase FTP site]; one can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
<br />
===9.17. Where can I find FlyBase data for older genome assemblies?===<br />
FlyBase archives the annotation files generated for every release on our [https://ftp.flybase.net/ FlyBase FTP site]. This includes FASTA and GFF for almost all past releases, and GTF files for Release 6 (dm6) releases. One can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172892FlyBase:FAQ2024-02-22T09:53:22Z<p>Arzu Ozturk Colak: /* 9.17. Where can I find FlyBase data for older genome assemblies? */</p>
<hr />
<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|-<br />
! style="text-align: left" | 9.17. !! style="text-align: left" | Where can I find FlyBase data for older genome assemblies?<br />
|-<br />
|style="text-align: left"| || FlyBase archives the annotation files (FASTA, GFF, GTF) generated for every release on our [https://ftp.flybase.net/releases/ FlyBase FTP site]; one can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Archives", and select "Other Archives".<br />
<br />
So, for example, from the archives page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
<br />
===9.17. Where can I find FlyBase data for older genome assemblies?===<br />
FlyBase archives the annotation files generated for every release on our [https://ftp.flybase.net/ FlyBase FTP site]. This includes FASTA and GFF for almost all past releases, and GTF files for Release 6 (dm6) releases. One can find the link to FTP archived release in the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Releases (FTP)".<br />
<br />
The full list of past FlyBase releases is available on our [https://flybase.org/downloads/archivedata Archived Data] page; one can find the link to the archived data page in the the blue navigation bar at the top of every FlyBase page - click on "Downloads", and select "Archived Data".<br />
<br />
So, for example, from the Archived Data page, one can look up the date of the final FlyBase release on the retired Release 5 (dm3) D. melanogaster genone assembly, which as FB2014_03 (May 2014, Dmel Release 5.57). Then, one can look up archived data for the FB2014_03 release on the FTP archives site.<br />
<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Community_Advisory_Group&diff=172622FlyBase:Community Advisory Group2023-11-27T14:38:50Z<p>Arzu Ozturk Colak: /* Surveys */</p>
<hr />
<div>==What is the FlyBase Community Advisory Group?==<br />
<br />
The FlyBase Community Advisory Group (FCAG) was launched in September 2014 with the aim of '''gaining greater feedback from the community''' about changes in FlyBase. <br />
<br />
You may not know that FlyBase is generated by a team of 32 people, working at Harvard, Indiana, New Mexico and Cambridge Universities. As the members of the FlyBase team work to improve the amount and usefulness of data in FlyBase, numerous questions arise regarding which data are the most important for Drosophila researchers and how we can most usefully present these data on the website. While we do our best to make changes that will be optimal for all Drosophila researchers, we wanted to be able to consult more widely so that we could be sure that our decisions would be helpful for the greatest number of people.<br />
<br />
'''The group consists of members from any lab worldwide that uses FlyBase as part of its research'''. The FCAG member can be the lab head, a postdoc, student, technician or anyone else who uses FlyBase and feels that they could contribute. FlyBase attracts users from a variety of different backgrounds and our members range from frequent FlyBase users to those who use FlyBase only occasionally or who work primarily with another organism.<br />
<br />
Members of the group are sent '''up to 6 surveys a year''' on a variety of different subjects (see the [[FlyBase:Community Advisory Group#Surveys|Surveys]] section below for details of subjects that have been covered so far).<br />
<br />
==Current membership==<br />
<br />
As of 15<sup>th</sup> November 2021 the FlyBase Community Advisory Group comprised '''890 fly researchers''' from '''46 different countries'''. <br />
<br />
[[File:FCAG members nov 2021 min.png|700px|thumb|left]]<br />
{| class="wikitable" style="text-align: center;"<br />
|-<br />
! Country !! Number of members !! Country !! Number of members<br />
|-<br />
| United States || 344 || Nigeria || 6<br />
|-<br />
| United Kingdom || 101 || Austria || 5<br />
|-<br />
| Germany || 66 || Chile || 5<br />
|-<br />
| China || 41 || Taiwan || 5<br />
|-<br />
| India || 39 || Netherlands || 4<br />
|-<br />
| France || 35 || Singapore || 4<br />
|-<br />
| Spain || 31 || Argentina || 3<br />
|-<br />
| Canada || 25 || New Zealland || 3<br />
|-<br />
| Japan || 20 || Norway || 3<br />
|-<br />
| Italy || 17 || Belgium || 2<br />
|-<br />
| Brazil || 13 || Malta || 2<br />
|-<br />
| Sweden || 11 || Pakistan || 2<br />
|-<br />
| Israel || 10 || Thailand || 2<br />
|-<br />
| Korea South || 10 || Ukraine || 2<br />
|-<br />
| Switzerland || 10 || Cyprus || 1<br />
|-<br />
| Australia || 9 || Czech Republic || 1<br />
|-<br />
| Portugal || 9 || Estonia || 1<br />
|-<br />
| Russian Federation || 9 || Lebanon || 2<br />
|-<br />
| Greece || 7 || Panama || 1<br />
|-<br />
| Hungary || 7 || Poland || 1<br />
|-<br />
| Denmark || 6|| South Africa || 1<br />
|-<br />
| Finland || 6 || Uganda || 1<br />
|-<br />
| Mexico || 6 || Turkey || 1<br />
|}<br />
<br />
==Joining the group==<br />
<br />
Every person who uses FlyBase in their research is welcome into our group. Our aim is to have at least a representative from every lab. If you are interested in joining FCAG please go to the [http://{{flybaseorg}}/static/fcag registration form]<br />
<br />
==Updating your details (current members)==<br />
<br />
If you are an existing member of the group and you would like to update your details click [http://{{flybaseorg}}/contact/email here] to go to our contact FlyBase form and choose the subject ‘FlyBase Community Advisory Group’, detailing the changes you would like to make.<br />
<br />
==Surveys==<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
!width="80"|Date<br />
!width="350"|Subject<br />
!width="10"|Responses<br />
! Results<br />
|-<br />
|style="text-align:center;" |Nov 2023<br />
|<br />
FlyBase Survey: Fly Lab List<br />
|style="text-align:center;" |<br />
274<br />
|<br />
[[File:FlyBase_Survey_-_Fly_Lab_List_.pdf ]]<br />
|-<br />
|-<br />
|style="text-align:center;" |July 2023<br />
|<br />
FlyBase Gene Ontology (GO) Survey<br />
|style="text-align:center;" |<br />
142<br />
|<br />
[[File: FlyBase Gene Ontology (GO) Survey.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Feb 2023<br />
|<br />
FlyBase Survey: 'Have you seen this?'<br />
|style="text-align:center;" |<br />
110<br />
|<br />
[[File: FlyBase Survey - Have you seen this.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Nov 2022<br />
|<br />
FlyBase Features for scRNAseq Data<br />
|style="text-align:center;" |<br />
111<br />
|<br />
[[File: FlyBase_Features_for_scRNAseq_Data.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2022<br />
|<br />
FlyBase ''Drosophila'' Metabolic Pathways<br />
|style="text-align:center;" |<br />
199<br />
|<br />
[[File: FB_Metabolic_Pathways.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Aug 2021<br />
|<br />
FlyBase OrthoDB<br />
|style="text-align:center;" |<br />
272<br />
|<br />
[[File: FB_OrthoDB.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2019<br />
|<br />
FlyBase gene summaries<br />
|style="text-align:center;" |<br />
81<br />
|<br />
[[File: FB_Gene_Summaries.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2019<br />
|<br />
FlyBase bulk data files<br />
|style="text-align:center;" |<br />
70<br />
|<br />
[[File: FB_bulk_data_files.pdf]]<br />
|-<br />
|style="text-align:center;" |May 2018<br />
|<br />
FlyBase 2.0<br />
|style="text-align:center;" |<br />
175<br />
|<br />
[[File: FlyBase_2.0.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2018<br />
|<br />
FlyBase Author Reagent Form<br />
|style="text-align:center;" |<br />
22<br />
|<br />
[[File: ART_survey.pdf]]<br />
|-<br />
|style="text-align:center;" |Dec 2017<br />
|<br />
Drosophila template for NCBI dataset submissions<br />
|style="text-align:center;" |<br />
97<br />
|<br />
[[File: FCAG BioSample template.pdf]]<br />
|-<br />
|style="text-align:center;" |Sept 2017<br />
|<br />
Curation of phenotypes induced or modified by chemical treatments or nutritional challenges<br />
|style="text-align:center;" |<br />
118<br />
|<br />
[[File: Chemical_and_nutritional_phenotype_curation.pdf]]<br />
|-<br />
|style="text-align:center;" |Jan 2017<br />
|<br />
GAL4 Search Improvements<br />
|style="text-align:center;" |<br />
157<br />
|<br />
[[File: GAL4 _Search_Improvements_Survey.pdf]]<br />
|-<br />
|style="text-align:center;" |Nov 2016<br />
|<br />
Display of Gene Ontology Annotations<br />
|style="text-align:center;" |<br />
172<br />
|<br />
[[File: Display of Gene Ontology Annotations survey.pdf]]<br />
|-<br />
|style="text-align:center;" |Sept 2016<br />
|<br />
2016 General FlyBase survey<br />
|style="text-align:center;" |<br />
235<br />
|<br />
[[File: 2016 General FlyBase survey.pdf]]<br />
|-<br />
|style="text-align:center;" |July 2016<br />
|<br />
Protein domain graphics/info<br />
|style="text-align:center;" |<br />
208<br />
|<br />
[[File: FCAGwikiProteinDomainSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | Jan 2016<br />
|<br />
Video tutorials<br />
|style="text-align:center;" |<br />
149<br />
|<br />
[[File: FCAGwikiVideoTutorialSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | Oct 2015<br />
|<br />
Predicting the future of fly research<br />
|style="text-align:center;" |<br />
135<br />
|<br />
[[File: FCAG_predicting_the_future.pdf]]<br />
|-<br />
|style="text-align:center;" | July 2015<br />
|<br />
Default tracks on GBrowse<br />
|style="text-align:center;" |<br />
198<br />
|<br />
[[File: GBrowse_default tracks survey results.pdf]]<br />
|-<br />
|style="text-align:center;" | May 2015<br />
|<br />
Complex mutants and transgenic constructs<br />
|style="text-align:center;" |<br />
274<br />
|<br />
[[File: FCAG_construct_survey_full_results.pdf]]<br />
|-<br />
|style="text-align:center;" | Jan 2015 <br />
| <br />
New 'Gene Group' resource<br />
|style="text-align:center;" |<br />
383<br />
|<br />
[[File: FCAG_GeneGroup_survey_results.pdf]]<br />
|-<br />
|style="text-align:center;" | Oct 2014 <br />
| <br />
* How you use FlyBase and how it could be improved<br />
* The automatically generated gene summaries on the gene report<br />
* Receiving updates from FlyBase<br />
|style="text-align:center;" |<br />
454<br />
|<br />
[[File: FCAG_introductory_survey_results.pdf]]<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=File:FlyBase_Survey_-_Fly_Lab_List_.pdf&diff=172621File:FlyBase Survey - Fly Lab List .pdf2023-11-27T14:38:09Z<p>Arzu Ozturk Colak: </p>
<hr />
<div></div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Allele_Report&diff=172595FlyBase:Allele Report2023-11-10T12:31:55Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>Last Updated: 29th May 2015<br />
<br />
The '''Allele Report''' contains the information for an individual allele.<br />
<br />
An allele is a variant of a gene, often induced by mutagenic means. An allele may be defined by genetic/phenotypic characteristics, e.g. by complementation analysis, or in terms of alterations mapped to the known sequence of that gene, or both.<br />
<br />
As well as including allele reports for classical mutant alleles and natural variants, e.g. electrophoretic variants, FlyBase also includes reports for alleles that have been introduced into Drosophila via transgenic constructs. See the [[FlyBase:Nontraditional_alleles|Nontraditional alleles]] documentation for a detailed description of these alleles.<br />
<br />
This is a field-by-field guide to the information provided in the Allele Report.<br />
<br />
FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication if they wish. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data. The exception in the '''Allele Report''' is the [[FlyBase:Allele Report#General Information|General Information]] section which contains a summary of the identity of the allele.<br />
<br />
==General Information==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
||'''Symbol''' || style="width: 80%;" | The valid symbol that is used in FlyBase for the allele.<br />
<br />
The first part of the symbol (before the '\') is the standard prefix for the species (from the [[FlyBase:Abbreviations|Species Abbreviations]] list). For species other than D.melanogaster, the species prefix is displayed wherever the allele symbol is used throughout FlyBase. For D.melanogaster alleles, the species prefix is only displayed in the [[FlyBase:Allele Report#General Information|General Information]] section at the top of a Report.<br />
|-<br />
|'''Name''' || The valid full name that is used in FlyBase for the allele.<br />
|-<br />
|'''Feature type''' || The type of feature described in the report. In this case, "allele".<br />
|-<br />
|'''Associated Insertion(s)''' || If the allele is associated with an insertion of DNA, the insertion symbol is displayed in this field. The inserted DNA may be a natural transposable element e.g. P-element, a transposable-element based transgenic construct, e.g. [http://{{flybaseorg}}/reports/FBtp0000204.html P{lacW}], or exogenous DNA inserted via non-transposable element-based means (e.g. homologous recombination), e.g. TI{GAL4}.<br />
<br />
Clicking on an insertion symbol will take you to the relevant [[FlyBase:Insertion Report|Insertion Report]].<br />
<br />
An allele is associated with an insertion if any one or more of the following criteria apply:<br />
<br />
- the insertion results in a mutant phenotype by affecting expression of the gene into which it is inserted<br />
<br />
- the insertion is within the transcribed extent of a gene<br />
<br />
- the allele represents an open reading frame carried in the insertion, where its expression is influenced by a regulatory region in the genome where it is inserted e.g. GAL4 enhancer trap allele.<br />
|-<br />
|'''Species''' || The organism that the allele originates from, with the initial letter of the genus and the full species name listed.<br />
|-<br />
|'''FlyBase ID''' || The '''Primary''' FlyBase identifier number of the allele, used to uniquely identify the allele in the database.<br />
<br />
An allele may also have any number of '''Secondary''' FlyBase identifier numbers, which are listed in the '''Secondary FlyBase IDs''' section of the '''Allele Report'''.<br />
|-<br />
|'''Associated gene''' || The gene which the mutant affects.<br />
<br />
Clicking on the gene symbol will take you to the relevant [[FlyBase:Gene Report|Gene Report]]<br />
|-<br />
|'''Carried in Construct''' || If the allele is carried in a transgenic construct, the transgenic construct symbol is displayed in this field. <br />
<br />
Clicking on a transgenic construct symbol will take you to the relevant [[FlyBase:Recombinant Construct Report|Recombinant Construct Report]].<br />
|-<br />
|'''Also Known As''' || A list of up to 10 commonly used symbol synonyms for the gene. (This list is made computationally, based on the frequency of alternative symbols that have been curated from the literature.). This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Key Links''' || Link to the corresponding page at the [http://www.alliancegenome.org/ Alliance of Genome Resources]<br />
|-<br />
|'''Genomic Maps (JBrowse)''' || A JBrowse image showing the location of the mutation on the genome. This field is only displayed if the allele, or an insertion associated with the allele, has been mapped to the genome.<br />
<br />
The "JBrowse" link goes to a fully interactive JBrowse view of the same region.<br />
|-<br />
|'''Allele class''' || A summary list (without the publications that were the source of the information) of [[FlyBase:Controlled_vocabularies_used_by_FlyBase|controlled vocabulary]] terms from the [https://github.com/FlyBase/flybase-controlled-vocabulary FlyBase controlled vocabulary] that describe the class of the allele, e.g. "hypomorph" or "gain of function".<br />
<br />
For a list of allele class terms together with the associated publications, see the Allele class field in the [[FlyBase:Allele Report#Nature of the Allele|Nature of the Allele]] section of the Allele Report.<br />
|-<br />
||'''Mutagen''' || A summary list (without the publications that were the source of the information) of [[FlyBase:Controlled_vocabularies_used_by_FlyBase|controlled vocabulary]] terms from the [https://github.com/FlyBase/flybase-controlled-vocabulary FlyBase controlled vocabulary] that describe the origin of the allele, typically the mutagen(s) used to induce the mutant allele or the type of in vitro mutagenesis method used to create it.<br />
<br />
For a list of mutagen terms together with the associated publications, see the Mutagen field in the [[FlyBase:Allele Report#Nature of the Allele|Nature of the Allele]] section of the '''Allele Report'''.<br />
<br />
|}<br />
<br />
==Nature of the Allele==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Allele class''' || style="width: 80%;" | A full list (including the publications that were the source of the information) of [[FlyBase:Controlled_vocabularies_used_by_FlyBase|controlled vocabulary]] terms from the [https://github.com/FlyBase/flybase-controlled-vocabulary FlyBase controlled vocabulary] that describe the class of the allele, e.g. "hypomorph" or "gain of function".<br />
|-<br />
|'''Mutagen''' || A full list (including the publications that were the source of the information) of [[FlyBase:Controlled_vocabularies_used_by_FlyBase|controlled vocabulary]] terms from the [https://github.com/FlyBase/flybase-controlled-vocabulary FlyBase controlled vocabulary] that describe the origin of the allele, typically the mutagen(s) used to induce the mutant allele or the type of in vitro mutagenesis method used to create it.<br />
|-<br />
|'''Mutations Mapped to the Genome - Curation Data''' || A table listing features associated with the allele that have been mapped to the genome and form part of the annotation of the gene. The table lists the type of feature in the first column. The second column contains its location on the genome. The third column lists the evidence type, any associated mapping information, and any comments related to mapping the feature. The fourth column lists the reference used to map the feature.<br />
|-<br />
|'''Mutations Mapped to the Genome - Variant Molecular Consequences''' || Variants data from FlyBase are run through the Ensembl [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4 VEP] (Variant Effect Predictor) pipeline, and the results are displayed in a table. The VEP algorithm considers the genomic location, mutation type, and nucleotide change of a variant to calculate the molecular consequence on all of the overlapping transcripts affected by the variant. In addition to reporting the molecular change to the transcripts and encoded CDS, it assigns a Sequence Ontology (SO)-based consequence term to each variant/transcript combination.<br />
<br />
The table displays, for each variant, all genes that are potentially affected by that variant, the allele associated with the variant that is the subject of the report, and the predicted consequences to all affected transcripts.<br />
<br />
This is the result of a collaboration between FlyBase, [https://www.alliancegenome.org/ Alliance of Genome Resources] and Ensembl.<br />
|-<br />
|'''Associated Sequence Data''' || A table of sequence accession numbers associated with the allele. Clicking on the accession number will take you to the appropriate entry in the external database from which they are derived.<br />
<br />
The table contains accession numbers from the following databases:<br />
<br />
[http://www.ddbj.nig.ac.jp/ DDBJ]/[http://www.ebi.ac.uk/ena EMBL]/[http://www.ncbi.nlm.nih.gov/genbank/ GenBank] - nucleic acid accession number and associated protein ID number (if applicable).<br />
<br />
[http://www.uniprot.org/ UniProtKB/Swiss-Prot] - protein accession number.<br />
<br />
[http://www.uniprot.org/ UniProtKB/TrEMBL] - protein accession number. <br />
<br />
These accession numbers are [[FlyBase:RefMan F.|FlyBase curated links]].<br />
|-<br />
|'''Progenitor genotype''' || For classical alleles, this is the mutant chromosome(s) on which the allele was induced, where the progenitor is relevant to the derivative allele. The progenitor is usually another mutant allele of the same gene, or a transposable element insertion.<br />
<br />
For [[FlyBase:Nontraditional_alleles|non-traditional alleles]] carried in transgenic constructs, this is typically the allele that was used in vitro as the progenitor.<br />
<br />
Clicking on the symbol of the progenitor will take you to the relevant '''Report page'''.<br />
|-<br />
|'''Caused by insertion''' || If the allele is associated with an insertion of DNA, the insertion symbol is displayed in this field. The inserted DNA may be a natural transposable element e.g. P-element, a transposable-element based transgenic construct, e.g. [http://{{flybaseorg}}/reports/FBtp0000204.html P{lacW}], or exogenous DNA inserted via non-transposable element-based means (e.g. homologous recombination), e.g. TI{GAL4}.<br />
<br />
Clicking on an insertion symbol will take you to the relevant [[FlyBase:Insertion Report|Insertion Report]].<br />
<br />
This field is only displayed on an individual Allele Report if it contains data. <br />
<br />
An allele is associated with an insertion if any one or more of the following criteria apply:<br />
<br />
- the insertion results in a mutant phenotype by affecting expression of the gene into which it is inserted<br />
<br />
- the insertion is within the transcribed extent of a gene<br />
<br />
- the allele represents an open reading frame carried in the insertion, where its expression is influenced by a regulatory region in the genome where it is inserted e.g. GAL4 enhancer trap allele.<br />
|-<br />
|'''Carried in construct''' || If the allele is carried in a transgenic construct, the transgenic construct symbol is displayed in this field.<br />
<br />
Clicking on a transgenic construct symbol will take you to the relevant [[FlyBase:Recombinant Construct Report|Recombinant Construct Report]].<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Cytology''' || Free text comments about the cytology of the allele.<br />
|-<br />
|'''Nature of the lesion''' || For classical alleles, this is a free text description of the nature of the mutant lesion.<br />
<br />
For [[FlyBase:Nontraditional_alleles|non-traditional alleles]] carried in transgenic constructs, this is a free text description of the overall structure of the allele at the end of the cloning process.<br />
|-<br />
|'''Associated Sequence Features''' || If the allele is associated with a sequence feature, such as an RNAi amplicon, the sequence feature symbol is displayed in this field. <br />
<br />
Clicking on a sequence feature symbol will take you to the relevant [[FlyBase:Sequence Feature Report|Sequence Feature Report]]. <br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Tags''' || This field is displayed in an Allele Report that represents an engineered tag which has been used in a transgenic construct to mark genes or their products. This includes variants of epitope tags such as the EGFP version of "Avic\GFP".<br />
<br />
The field lists the alleles that contain the tag.<br />
<br />
Clicking on the symbol will take you to the relevant Allele Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Tagged with''' || This field is only filled in for [[FlyBase:Nontraditional_alleles|non-traditional alleles]] carried in transgenic constructs. If the allele contains an engineered tag that has been used to mark the gene or its product, the symbol of that tag is displayed in this field.<br />
<br />
Engineered tags include epitope tags such as "Avic\GFP" and function tags such as nuclear localization signals.<br />
<br />
Clicking on the tag symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Caused by aberration''' || If the allele is caused by an aberration breakpoint within the locus, the aberration symbol is displayed in this field.<br />
<br />
Clicking on the aberration symbol will take you to the relevant [[FlyBase:Aberration Report|Aberration Report]].<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|}<br />
<br />
==Expression Data==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Reporter Expression''' || style="width: 80%;" | A three column table with the headings Stage, Tissue/Position, and Reference. Each row in the table represents one distinct expression pattern defined by time of expression (Stage) and by location of expression (Tissue/Position). Each distinct expression pattern is attributed to the reference that reported it. Developmental stages and anatomical parts are described using controlled vocabulary (CV) terms (for valid CV terms, see the [http://{{flybaseorg}}/vocabularies Vocabularies] search page). <br />
<br />
The table is subdivided by the assay, when appropriate.<br />
<br />
|-<br />
|'''Additional information''' || <br />
Free-text curated descriptions of expression patterns, sorted by reference.<br />
|}<br />
<br />
==Human Disease Associations==<br />
<br />
===Disease Ontology (DO) Annotations===<br />
<br />
Human Disease model data curated using disease terms from the [http://disease-ontology.org/ Disease Ontology]. <br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Models Based on Experimental Evidence''' || style="width: 80%;" | A table showing any human disease(s) that are being modelled by a given mutant or transgenic allele. The phenotype(s) being studied must recapitulate some aspect of the human disease for the allele to be considered a model. In some cases, an allele may be expected to produce a disease phenotype but does not. These unexpectedly negative results are also shown. <br />
<br />
The table consists of three columns<br />
<br />
'''Disease''' - Indicates whether or not the allele is modeling the disease ('model of' or ''''DOES NOT''' model') followed by the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]).<br />
<br />
'''Evidence''' - '''CEA''' (combinatorial experimental and author inference evidence used in manual assertion; ECO:0007013) is used when an annotation is made based on experimental evidence AND the disease term used agrees with that stated by the authors. This is the most commonly used evidence code. '''CEC''' (combinatorial experimental and curator inference evidence used in manual assertion; ECO:0007014) is used when an annotation is made based on experimental evidence BUT the disease term used has been determined by a curator rather than based on a statement by the authors of the paper. Use of this evidence code is relatively rare, restricted to cases where (i) the disease stated by the authors is relatively general (e.g. “amyotrophic lateral sclerosis”), but the curator can provide a more specific subtype (e.g. “amyotrophic lateral sclerosis type 6”) based on the given human gene/variant and its known relationship to a specific disease (e.g. in OMIM); or (ii) the authors have made a mistake in the given gene-to-disease relationship. If the given allele only models the disease in combination with another allele, the word '''with''' is displayed followed by the symbols of other allele(s), with hyperlinks to the relevant allele report pages. Note that any drivers that are required for the expression of transgenic alleles are not listed in this section.<br />
<br />
'''References''' - lists the reference(s) that describe the model.<br />
|-<br />
|'''Modifiers Based on Experimental Evidence''' || A table showing interactions of this allele with other disease-causing allele(s)<br />
<br />
The table consists of three columns<br />
<br />
'''Disease''' - the nature of the interaction ('exacerbates' or 'ameliorates' and the name of the disease (from the [http://disease-ontology.org/ Disease Ontology]). This column also indicates if the allele is not modifying a disease (prefixed with '''DOES NOT''').<br />
<br />
'''Interaction''' - 'modeled by' followed by the symbol of the allele that is modeling the disease, with hyperlinks to the relevant allele report pages. <br />
<br />
'''References''' - lists the reference(s) that describes the model.<br />
|-<br />
|'''Comments on Models/Modifiers Based on Experimental Evidence''' || Curated comments that highlight certain features of a model, for example, when particular aspects of a disease phenotype are modeled while others are not. These comments are used sparingly to avoid duplication with phenotype information.<br />
|}<br />
<br />
==Phenotypic Data==<br />
<br />
===Phenotypic Class===<br />
<br />
A list of statements describing the overall phenotypic class of the mutant allele.<br />
<br />
Each statement contains a controlled vocabulary term from the [http://{{flybaseorg}}/cgi-bin/cvreport.pl?rel=is_a&id=FBcv:0000347 phenotypic class] section of the FlyBase controlled vocabulary that describes the class of phenotype that is observed in the mutant allele, e.g. visible, lethal, circadian rhythm defective.<br />
<br />
The phenotypic class term may also be "qualified" with more controlled vocabulary term(s) that further specify the mutant phenotype, for example, describing whether the phenotype is "recessive" or "dominant", or specifying at which stage of development the phenotype is observed, e.g. second instar larval stage. These additional qualifying terms are either from the FlyBase controlled vocabulary or the Development controlled vocabulary.<br />
<br />
If the mutant phenotype is observed in combination with another allele of the same gene, or a deficiency that affects the same gene, this second allele or deficiency is indicated in parentheses after the controlled vocabulary terms. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is indicated at the end of the phenotypic class statement, after a comma.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
===Phenotype Manifest In===<br />
<br />
A list of the parts of the animal affected by the mutant allele. These terms range from the entire animal to subcellular components and are often specific for a developmental stage. Body part and cell-type terms are from the Anatomy controlled vocabulary, while terms relating to parts of the cell are cellular component terms from the Gene Ontology controlled vocabulary.<br />
<br />
The body part term may also be "qualified" with more controlled vocabulary term(s) that further specify the mutant phenotype, for example, describing that the body part was affected in an experiment involving a "somatic clone" or is due to a "maternal effect". These additional qualifying terms are from the FlyBase controlled vocabulary.<br />
<br />
If the mutant phenotype is observed in combination with another allele of the same gene, or a deficiency that affects the same gene, this second allele or deficiency is indicated in parentheses after the controlled vocabulary terms. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is indicated at the end of the phenotypic class statement, after a comma.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
===Detailed Description===<br />
<br />
Free text description providing additional context to the mutant phenotype.<br />
As of FB2022_04 release we've stopped providing free text description to get better overall data coverage using robustly searchable controlled vocabulary statements. Free text descriptions captured prior to FB2022_04 release will still be displayed.<br />
<br />
===External Data===<br />
A list of additional links to external databases that are relevant to phenotypic data is also displayed.<br />
<br />
==Interactions==<br />
<br />
Clicking on the 'Enhancers & Suppressors' button shows you shows you the genetic interaction network for this allele in the [http://{{flybaseorg}}/cgi-bin/get_interactions.html Interactions Browser]<br />
<br />
===Phenotypic Class===<br />
<br />
<br />
====Enhanced by====<br />
<br />
A list of statements describing phenotypes of this allele that are enhanced by a mutation in another gene.<br />
<br />
The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic class subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report, but in addition, the nature of the interaction (in this case "enhanceable by") and the interacting genotype are listed at the end of the statement.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====NOT Enhanced by====<br />
<br />
A list of statements describing phenotypes of this allele that are '''NOT''' enhanced by a mutation in another gene.<br />
<br />
The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic class subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report, but in addition, the nature of the interaction (in this case "non-enhanceable by") and the interacting genotype are listed at the end of the statement.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====Suppressed by====<br />
<br />
A list of statements describing phenotypes of this allele that are suppressed by a mutation in another gene.<br />
<br />
The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic class subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report, but in addition, the nature of the interaction (in this case "suppressible by") and the interacting genotype are listed at the end of the statement.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====NOT Suppressed by====<br />
<br />
A list of statements describing phenotypes of this allele that are '''NOT''' suppressed by a mutation in another gene.<br />
<br />
The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the [[FlyBase:Allele Report#Phenotypic Class|Phenotypic class]] subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report, but in addition, the nature of the interaction (in this case "non-suppressible by") and the interacting genotype are listed at the end of the statement.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====Enhancer of====<br />
<br />
A list of statements describing phenotypes of a mutation in another gene that this allele enhances.<br />
<br />
Each statement starts with the nature of the interaction (in this case "enhancer"), followed by the phenotype that is being enhanced and then the genotype that is being enhanced.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====NOT Enhancer of====<br />
<br />
A list of statements describing phenotypes of a mutation in another gene that this allele '''DOES NOT''' enhance.<br />
<br />
Each statement starts with the nature of the interaction (in this case "non-enhancer"), followed by the phenotype that is not enhanced and then the genotype that is not enhanced.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====Suppressor of====<br />
<br />
A list of statements describing phenotypes of a mutation in another gene that this allele suppresses.<br />
<br />
Each statement starts with the nature of the interaction (in this case "suppressor"), followed by the phenotype that is being suppressed and then the genotype that is being suppressed.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====NOT Suppressor of====<br />
<br />
A list of statements describing phenotypes of a mutation in another gene that this allele '''DOES NOT''' suppress.<br />
<br />
Each statement starts with the nature of the interaction (in this case "non-suppressor"), followed by the phenotype that is not suppressed and then the genotype that is not suppressed.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====Other====<br />
<br />
A list of statements describing phenotypes involving alleles of more than one gene (including this allele), where it is known that there is an interaction between the alleles, but either the nature of the interaction is not known, or each single mutant by itself does not show a mutant phenotype. Each statement lists the phenotype seen in the double mutant genotype, followed by the interacting allele.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic class subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
===Phenotype Manifest In===<br />
<br />
====Enhanced by====<br />
<br />
A list of body parts where the phenotype for this allele is manifest, for which each phenotype is enhanced by a mutation in another gene.<br />
<br />
The body part affected is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic manifest in subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report, but in addition, the nature of the interaction (in this case "enhanceable by") and the interacting genotype are listed at the end of the statement.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====NOT Enhanced by====<br />
<br />
A list of body parts where the phenotype for this allele is manifest, for which each phenotype is NOT enhanced by a mutation in another gene.<br />
<br />
The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic manifest in subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report, but in addition, the nature of the interaction (in this case "non-enhanceable by") and the interacting genotype are listed at the end of the statement.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====Suppressed by====<br />
<br />
A list of body parts where the phenotype for this allele is manifest, for which each phenotype is suppressed by a mutation in another gene.<br />
<br />
The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic manifest in subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report, but in addition, the nature of the interaction (in this case "suppressible by") and the interacting genotype are listed at the end of the statement.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====NOT Suppressed by====<br />
<br />
A list of body parts where the phenotype for this allele is manifest, for which each phenotype is NOT suppressed by a mutation in another gene.<br />
<br />
The phenotype is described using controlled vocabulary terms, with the same syntax as that used in the Phenotypic manifest in subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report, but in addition, the nature of the interaction (in this case "non-suppressible by") and the interacting genotype are listed at the end of the statement.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====Enhancer of====<br />
<br />
A list of body parts where the phenotype for a mutation in another gene is manifest, for which each phenotype is enhanced by this allele.<br />
<br />
Each statement starts with the nature of the interaction (in this case "enhancer"), followed by the phenotype that is being enhanced and then the genotype that is being enhanced.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic manifest in subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====NOT Enhancer of====<br />
<br />
A list of body parts where the phenotype for a mutation in another gene is manifest, for which each phenotype is NOT enhanced by this allele.<br />
<br />
Each statement starts with the nature of the interaction (in this case "non-enhancer"), followed by the phenotype that is not enhanced and then the genotype that is not enhanced.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic manifest in subsection of the [[[FlyBase:Allele report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====Suppressor of====<br />
<br />
A list of body parts where the phenotype for a mutation in another gene is manifest, for which each phenotype is suppressed by this allele.<br />
<br />
Each statement starts with the nature of the interaction (in this case "suppressor"), followed by the phenotype that is being suppressed and then the genotype that is being suppressed.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic manifest in subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====NOT Suppressor of====<br />
<br />
A list of body parts where the phenotype for a mutation in another gene is manifest, for which each phenotype is NOT suppressed by this allele.<br />
<br />
Each statement starts with the nature of the interaction (in this case "non-suppressor"), followed by the phenotype that is not suppressed and then the genotype that is not suppressed.<br />
<br />
The phenotype is described using controlled vocabulary terms, with a similar syntax to that used in the Phenotypic manifest in subsection of the [[FlyBase:Allele Report#Phenotypic Data|Phenotypic Data]] section of the Allele Report.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
====Other====<br />
<br />
A list of statements describing phenotypes involving alleles of more than one gene (including this allele), where it is known that there is an interaction between the alleles, but either the nature of the interaction is not known, or each single mutant by itself does not show a mutant phenotype. Each statement lists the body part affected in the double mutant genotype, followed by the interacting allele.<br />
<br />
Clicking on a controlled vocabulary term will take you to the relevant [[FlyBase:Vocabularies|CV Term Report]].<br />
<br />
Clicking on an allele or deficiency symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
<br />
===Additional Comments===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Genetic Interactions''' || style="width: 80%;" | Free text description providing additional context to the genetic interactions involving the allele. Genetic interactions are defined in FlyBase as interactions between alleles of genes derived from the same species that the interaction is being assayed in.<br />
As of FB2018_05 release we've stopped providing free text description to get better overall data coverage using robustly searchable controlled vocabulary statements. Free text descriptions captured prior to FB2018_05 release will still be displayed.<br />
|-<br />
|'''Xenogenetic Interactions''' || Free text description providing additional context to the xenogenetic interactions involving the allele. Xenogenetic interactions are defined in FlyBase as either interactions between alleles of genes not normally found in the same species, or interactions being assayed in a species that is not the one in which either of the interacting genes is normally found.<br />
As of FB2018_05 release we've stopped providing free text description to get better overall data coverage using robustly searchable controlled vocabulary statements. Free text descriptions captured prior to FB2018_05 release will still be displayed.<br />
|}<br />
<br />
==Complementation & Rescue Data==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Complements''' || style="width: 80%;" | A list of alleles reported to be complemented by this allele, where both are alleles of the same gene.<br />
<br />
Clicking on an allele symbol will take you to the relevant Allele Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Partially complements''' || A list of alleles reported to be partially complemented by this allele, where both are alleles of the same gene.<br />
<br />
Clicking on an allele symbol will take you to the relevant Allele Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Fails to complement''' || A list of alleles reported '''NOT''' to be complemented by this allele, where both are alleles of the same gene.<br />
<br />
Clicking on an allele symbol will take you to the relevant Allele Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Rescued by''' || A list of alleles reported to rescue this allele, where both are alleles of the same gene. If the rescue experiment used a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated.<br />
<br />
Clicking on a symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Partially rescued by''' || A list of alleles reported to partially rescue this allele, where both are alleles of the same gene. If the rescue experiment used a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated.<br />
<br />
Clicking on a symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Not rescued by''' || A list of alleles reported NOT to rescue this allele, where both are alleles of the same gene. If the rescue experiment used a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated.<br />
<br />
Clicking on a symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Rescues''' || A list of mutations of the same gene as this allele (typically another allele of the same gene, or a deficiency that affects the same gene) reported to be rescued by this allele. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated.<br />
<br />
Clicking on a symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Partially rescues''' || A list of mutations of the same gene as this allele (typically another allele of the same gene, or a deficiency that affects the same gene) reported to be partially rescued by this allele. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated.<br />
<br />
Clicking on a symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Fails to rescue''' || A list of mutations of the same gene as this allele (typically another allele of the same gene, or a deficiency that affects the same gene) reported NOT to be rescued by this allele. If the allele is part of a system that requires a driver, such as the UAS-GAL4 system, the driver allele is also indicated.<br />
<br />
Clicking on a symbol will take you to the relevant Report.<br />
<br />
This field is only displayed on an individual Allele Report if it contains data.<br />
|-<br />
|'''Comments''' || Free text description providing additional context to the complementation and rescue data.<br />
As of FB2018_05 release we've stopped providing free text description to get better overall data coverage using robustly searchable controlled vocabulary statements. Free text descriptions captured prior to FB2018_05 release will still be displayed.<br />
|}<br />
<br />
==Images==<br />
<br />
Where available, this section contains any images relevant to the allele.<br />
<br />
==Stocks==<br />
<br />
A list of experimental lines relating to this allele that are available for order from public stock centers.<br />
<br />
==Notes on Origin==<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|-<br />
|'''Discoverer''' || style="width: 80%;" | A list of the individuals who identified or generated the allele.<br />
|}<br />
<br />
Free text comments about the origin of the allele.<br />
<br />
For example, information that it was simultaneously induced with another mutation, or information about the genotype of the progenitor which is irrelevant to the derivative.<br />
<br />
==Comments==<br />
<br />
Miscellaneous free text comments about the allele.<br />
<br />
==Synonyms and Secondary IDs==<br />
<br />
===Reported As===<br />
<br />
{| class="wikitable" style="width: 100%;"<br />
|'''Symbol Synonym''' || style="width: 80%;" | A list of symbols that have been used in the literature, or by FlyBase, to describe the allele.<br />
|-<br />
|'''Name Synonym''' || A list of names that have been used in the literature, or by FlyBase, to describe the allele.<br />
|}<br />
<br />
===Secondary FlyBase IDs===<br />
<br />
A list of '''Secondary''' FlyBase identifier numbers of the allele.<br />
<br />
If an allele has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database.<br />
<br />
== References==<br />
<br />
A list of publications that discuss the allele, subdivided into fields by type of publication. Only fields containing data are displayed in an individual Allele Report.</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=172550FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2023-10-18T12:36:53Z<p>Arzu Ozturk Colak: /* Posters */</p>
<hr />
<div>== Presentations (Talks from Meetings or Courses) ==<br />
* CanFly 2023, June 2023. New and Classic Features in FlyBase. [[Media:Canfly2023-compressed_2.pdf | presentation]] (15 slides)<br />
* London Fly Meeting, October 2022. Exploiting single-cell RNA-sequencing data in FlyBase and the Single-Cell Expression Atlas. [[Media:London_Fly_Meeting_2022-scRNAseq_in_FlyBase_and_SCEA.pdf | presentation]] (26 slides)<br />
* CDRC 2021. Tools for Drosophila Research. [[Media:CDRC_2021_FlyBase.pdf|presentation]] (17 slides)<br />
* ADRC 2021. FlyBase updates 2021. [[Media:FlyBase_2021_updates.pdf|presentation]] (31 slides)<br />
* Boston Area Drosophila Meeting, June 2020. "Disease-relevant" to disease model: how FlyBase can help you investigate human disease in Drosophila. [[Media:BADM 2020 disease model talk-compressed.pdf|presentation]] (18 slides)<br />
* CanFly XV, June 2019. What's new in FlyBase? [[Media:CanFly2019.pdf|presentation]] (35 slides)<br />
* Boston Area Drosophila Meeting, June 2019. FlyBase Updates: Exploring the spectrum of Experimental Tools on FlyBase. [[Media:BADM_2019.pdf|presentation]] (11 slides)<br />
* ISB 2019. Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. [[Media:Biocurator2019_enzyme_talk.pdf|presentation]] (10 slides)<br />
* ADRC 2019. FlyBase updates 2019. [[Media:FlyBase updates 2019.pdf|presentation]] (18 slides)<br />
* Cambridge Fly Symposium, January 2019. Large-scale queries of FlyBase. [[Media:Large-scale queries of FlyBase.pdf|presentation]] (40 slides)<br />
* London Fly Meeting, April 2018. FlyBase 2018: New look, new features. [[Media:LFM_April2017.ppt|presentation]] (41 slides)<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* EDRC 2023. What's new: FlyBase updates. [[Media:EDRC2023_Whats_new.jpg|jpg]]<br />
* EDRC 2023. Outreach: FlyBase outreach resources. [[Media:EDRC2023_Outreach.jpg|jpg]]<br />
* EDRC 2023. FlyCyc: updating the metabolic network for Drosophila melanogaster. [[Media:FlyCyc_EDRC2023_poster.pdf|pdf]]<br />
* ISB 2023. Capturing the experimental research history of signalling pathways in Drosophila melanogaster. [[Media:Pathway-poster-for-ISB2023.pdf|pdf]]<br />
* ISB 2023. FlyCyc: updating the metabolic network for Drosophila melanogaster. [[Media:Marygold_ISB_2023.pdf|pdf]]<br />
* ADRC 2023. Exploiting single-cell RNA-sequencing data in FlyBase. [[Media:ADRC2023_Poster.pdf | pdf]]<br />
* ADRC 2021. Progress towards functional understanding of the gene repertoire of Drosophila. [[Media:Poster_ADRC2021_hattrill-compressed.pdf|pdf]]<br />
**Supplemental table of GO annotation count for protein-coding genes. [[Media:ADRC_2021_understudied_genes.xlsx|xlsx]]<br />
* ADRC 2021. An enzyme catalog for Drosophila melanogaster. [[Media:Marygold_531C_ePoster.pdf|pdf]]<br />
* TAGC 2020. What's new in FlyBase. [[Media:TAGC2020_whats_new.pdf|pdf]]<br />
* EDRC 2019. Systematising knowledge of Drosophila pathway members to fuel biological discovery. [[Media:EDRC2019-Pathways.pdf|pdf]]<br />
* EDRC 2019. What's New in FlyBase. [[Media:EDRC_2019_whats_new.pdf|pdf]]<br />
* ISB 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ISB2019-Pathways.pdf|pdf]]<br />
* ISB 2019. Experimental tools: a new way to categorise transgenic alleles in FlyBase. [[Media:ISB2019_experimental_tools.pdf|pdf]]<br />
* ISB 2019. The Drosophila Anatomy Ontology. [[Media:ISB2019_DAO.pdf|pdf]]<br />
* ADRC 2019. FlyBase: A Valuable Source of Molecular Interaction Data. [[Media:fb_poster.pdf|pdf]]<br />
* ADRC 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ADRC_2019_Pathways.pdf|pdf]]<br />
* ADRC 2019. Finding Human disease models in FlyBase: You can get there from here. [[Media:Disease_Navigation_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Finding GAL4 drivers and other transgenic tools in FlyBase. [[Media:GAL4_and_Tools_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Improving enzyme annotation in FlyBase. [[Media:Enzymes_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2018. FlyBase 2.0 - What’s new? [[Media:VitorADRC2018-FB_2.0_whatsnew.pdf|pdf]]<br />
* ADRC 2018. FlyBase & Community. [[Media:VitorADRC2018-FBandCommunity.pdf|pdf]]<br />
* ADRC 2018. Functional Annotation of Enzymes in FlyBase. [[Media:Phani_ADRC_2018.pdf|pdf]]<br />
* ADRC 2018. Finding GAL4 Drivers in FlyBase. [[Media:Gramates_GAL4_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* ISB 2018. FlyBase Representative Publications: using annotation data to identify key papers on a gene. [[Media:ISB-2018-poster-Representative-Publications.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* EDRC 2017. Function-centered approaches for finding and analyzing genes within FlyBase. [[Media:EDRC_poster_function.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
== Pamphlets and Handouts ==<br />
* ADRC 2019. New tools, features, and resources for 2019. [[Media:ADRC2019_NewTools.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
== Assorted FlyBase Help Presentations ==<br />
<br />
* 2021. Getting Stocks for Gene Lists. [[Media:Getting stocks for gene lists.pdf|pdf]] (15 slides)<br />
<br />
[[Category:DONE]]</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=172549FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2023-10-18T12:35:58Z<p>Arzu Ozturk Colak: /* Posters */</p>
<hr />
<div>== Presentations (Talks from Meetings or Courses) ==<br />
* CanFly 2023, June 2023. New and Classic Features in FlyBase. [[Media:Canfly2023-compressed_2.pdf | presentation]] (15 slides)<br />
* London Fly Meeting, October 2022. Exploiting single-cell RNA-sequencing data in FlyBase and the Single-Cell Expression Atlas. [[Media:London_Fly_Meeting_2022-scRNAseq_in_FlyBase_and_SCEA.pdf | presentation]] (26 slides)<br />
* CDRC 2021. Tools for Drosophila Research. [[Media:CDRC_2021_FlyBase.pdf|presentation]] (17 slides)<br />
* ADRC 2021. FlyBase updates 2021. [[Media:FlyBase_2021_updates.pdf|presentation]] (31 slides)<br />
* Boston Area Drosophila Meeting, June 2020. "Disease-relevant" to disease model: how FlyBase can help you investigate human disease in Drosophila. [[Media:BADM 2020 disease model talk-compressed.pdf|presentation]] (18 slides)<br />
* CanFly XV, June 2019. What's new in FlyBase? [[Media:CanFly2019.pdf|presentation]] (35 slides)<br />
* Boston Area Drosophila Meeting, June 2019. FlyBase Updates: Exploring the spectrum of Experimental Tools on FlyBase. [[Media:BADM_2019.pdf|presentation]] (11 slides)<br />
* ISB 2019. Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. [[Media:Biocurator2019_enzyme_talk.pdf|presentation]] (10 slides)<br />
* ADRC 2019. FlyBase updates 2019. [[Media:FlyBase updates 2019.pdf|presentation]] (18 slides)<br />
* Cambridge Fly Symposium, January 2019. Large-scale queries of FlyBase. [[Media:Large-scale queries of FlyBase.pdf|presentation]] (40 slides)<br />
* London Fly Meeting, April 2018. FlyBase 2018: New look, new features. [[Media:LFM_April2017.ppt|presentation]] (41 slides)<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* EDRC 2023. What's new: FlyBase updates. [[Media:EDRC2023_Whats_new.jpg|jpg]]<br />
* EDRC 2023. Outreach: FlyBase outreach resources. [[EDRC2023_Outreach.jpg|jpg]]<br />
* EDRC 2023. FlyCyc: updating the metabolic network for Drosophila melanogaster. [[Media:FlyCyc_EDRC2023_poster.pdf|pdf]]<br />
* ISB 2023. Capturing the experimental research history of signalling pathways in Drosophila melanogaster. [[Media:Pathway-poster-for-ISB2023.pdf|pdf]]<br />
* ISB 2023. FlyCyc: updating the metabolic network for Drosophila melanogaster. [[Media:Marygold_ISB_2023.pdf|pdf]]<br />
* ADRC 2023. Exploiting single-cell RNA-sequencing data in FlyBase. [[Media:ADRC2023_Poster.pdf | pdf]]<br />
* ADRC 2021. Progress towards functional understanding of the gene repertoire of Drosophila. [[Media:Poster_ADRC2021_hattrill-compressed.pdf|pdf]]<br />
**Supplemental table of GO annotation count for protein-coding genes. [[Media:ADRC_2021_understudied_genes.xlsx|xlsx]]<br />
* ADRC 2021. An enzyme catalog for Drosophila melanogaster. [[Media:Marygold_531C_ePoster.pdf|pdf]]<br />
* TAGC 2020. What's new in FlyBase. [[Media:TAGC2020_whats_new.pdf|pdf]]<br />
* EDRC 2019. Systematising knowledge of Drosophila pathway members to fuel biological discovery. [[Media:EDRC2019-Pathways.pdf|pdf]]<br />
* EDRC 2019. What's New in FlyBase. [[Media:EDRC_2019_whats_new.pdf|pdf]]<br />
* ISB 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ISB2019-Pathways.pdf|pdf]]<br />
* ISB 2019. Experimental tools: a new way to categorise transgenic alleles in FlyBase. [[Media:ISB2019_experimental_tools.pdf|pdf]]<br />
* ISB 2019. The Drosophila Anatomy Ontology. [[Media:ISB2019_DAO.pdf|pdf]]<br />
* ADRC 2019. FlyBase: A Valuable Source of Molecular Interaction Data. [[Media:fb_poster.pdf|pdf]]<br />
* ADRC 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ADRC_2019_Pathways.pdf|pdf]]<br />
* ADRC 2019. Finding Human disease models in FlyBase: You can get there from here. [[Media:Disease_Navigation_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Finding GAL4 drivers and other transgenic tools in FlyBase. [[Media:GAL4_and_Tools_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Improving enzyme annotation in FlyBase. [[Media:Enzymes_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2018. FlyBase 2.0 - What’s new? [[Media:VitorADRC2018-FB_2.0_whatsnew.pdf|pdf]]<br />
* ADRC 2018. FlyBase & Community. [[Media:VitorADRC2018-FBandCommunity.pdf|pdf]]<br />
* ADRC 2018. Functional Annotation of Enzymes in FlyBase. [[Media:Phani_ADRC_2018.pdf|pdf]]<br />
* ADRC 2018. Finding GAL4 Drivers in FlyBase. [[Media:Gramates_GAL4_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* ISB 2018. FlyBase Representative Publications: using annotation data to identify key papers on a gene. [[Media:ISB-2018-poster-Representative-Publications.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* EDRC 2017. Function-centered approaches for finding and analyzing genes within FlyBase. [[Media:EDRC_poster_function.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
== Pamphlets and Handouts ==<br />
* ADRC 2019. New tools, features, and resources for 2019. [[Media:ADRC2019_NewTools.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
== Assorted FlyBase Help Presentations ==<br />
<br />
* 2021. Getting Stocks for Gene Lists. [[Media:Getting stocks for gene lists.pdf|pdf]] (15 slides)<br />
<br />
[[Category:DONE]]</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=File:EDRC2023_Outreach.jpg&diff=172548File:EDRC2023 Outreach.jpg2023-10-18T12:34:59Z<p>Arzu Ozturk Colak: </p>
<hr />
<div></div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=File:EDRC2023_Whats_new.jpg&diff=172547File:EDRC2023 Whats new.jpg2023-10-18T12:29:29Z<p>Arzu Ozturk Colak: </p>
<hr />
<div></div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FlyBase_Guides:_Pamphlets,_Powerpoints,_and_Posters&diff=172546FlyBase:FlyBase Guides: Pamphlets, Powerpoints, and Posters2023-10-18T12:16:28Z<p>Arzu Ozturk Colak: /* Posters */</p>
<hr />
<div>== Presentations (Talks from Meetings or Courses) ==<br />
* CanFly 2023, June 2023. New and Classic Features in FlyBase. [[Media:Canfly2023-compressed_2.pdf | presentation]] (15 slides)<br />
* London Fly Meeting, October 2022. Exploiting single-cell RNA-sequencing data in FlyBase and the Single-Cell Expression Atlas. [[Media:London_Fly_Meeting_2022-scRNAseq_in_FlyBase_and_SCEA.pdf | presentation]] (26 slides)<br />
* CDRC 2021. Tools for Drosophila Research. [[Media:CDRC_2021_FlyBase.pdf|presentation]] (17 slides)<br />
* ADRC 2021. FlyBase updates 2021. [[Media:FlyBase_2021_updates.pdf|presentation]] (31 slides)<br />
* Boston Area Drosophila Meeting, June 2020. "Disease-relevant" to disease model: how FlyBase can help you investigate human disease in Drosophila. [[Media:BADM 2020 disease model talk-compressed.pdf|presentation]] (18 slides)<br />
* CanFly XV, June 2019. What's new in FlyBase? [[Media:CanFly2019.pdf|presentation]] (35 slides)<br />
* Boston Area Drosophila Meeting, June 2019. FlyBase Updates: Exploring the spectrum of Experimental Tools on FlyBase. [[Media:BADM_2019.pdf|presentation]] (11 slides)<br />
* ISB 2019. Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. [[Media:Biocurator2019_enzyme_talk.pdf|presentation]] (10 slides)<br />
* ADRC 2019. FlyBase updates 2019. [[Media:FlyBase updates 2019.pdf|presentation]] (18 slides)<br />
* Cambridge Fly Symposium, January 2019. Large-scale queries of FlyBase. [[Media:Large-scale queries of FlyBase.pdf|presentation]] (40 slides)<br />
* London Fly Meeting, April 2018. FlyBase 2018: New look, new features. [[Media:LFM_April2017.ppt|presentation]] (41 slides)<br />
* ADRC 2018. Finding your way around large-scale datasets and single-cell technologies. [[Media:ADRC2018_Datasets.pdf|presentation]] (19 slides)<br />
* ADRC 2018. FlyBase 2018: New look, new features. [[Media:FlyBase_2018_New_look_new_features.pdf|presentation]] (34 slides)<br />
* Cambridge (UK) Fly Club, October 2017. What's new in FlyBase. [[Media:Cambridge_UK_Fly_Club_Oct2017.pdf|presentation]] (42 slides)<br />
* ADRC 2017. What's new in FlyBase (in its 25th year). [[Media:ADRC2017_Whats_New_platform.pdf|presentation]] (18 slides)<br />
* ADRC 2017. New Features in FlyBase: FlyBase 2.0 (beta). [[Media:ADRC2017_New_Features_FlyBase2.0.pdf|presentation]] (22 slides)<br />
* ADRC 2017. Reaching across the MODs: enhanced orthology data and future prospects. [[Media:ADRC2017_Orthology_Across_Model_Organisms.pdf|presentation]] (36 slides)<br />
* TAGC/ADRC 2016. What's New in FlyBase. [[Media:TAGC_2016_FlyBase.pdf|presentation]] (24 slides)<br />
* EDRC 2015. What's New in FlyBase?. [[Media:EDRC_2015_FlyBase.pptx|presentation]] (29 slides)<br />
* ADRC 2015. New views in GBrowse2: Release 6 D. melanogaster assembly, RNA-Seq data, and more. [[Media:ADRC2015_GBrowse2_Release6.pdf|presentation]] (40 slides)<br />
* ADRC 2015. Human Disease models and Gene Groups. [[Media:ADRC2015_Disease_Models_&_Gene_Groups.pdf|presentation]] (20 slides)<br />
* ADRC 2014. Navigating High Throughput Data in FlyBase. [[Media:ADRC2014_HT_Data_Final.pdf|presentation]] (42 slides)<br />
* ADRC 2014. Human health-related models in Drosophila. [[Media:ADRC2014_human_health_related_models_in_drosophila.pptx|presentation]] (24 slides)<br />
* ADRC 2012. How High-Throughput Data Are Informing Gene Models. [[Media:HTD to gene models.ppt|presentation]] (66 slides)<br />
* ADRC 2010. Getting the most out of FlyBase. [[Media:ADRC2010 GetTheMostOutofFlyBase.ppt|presentation]] (46 slides)<br />
* ADRC 2010. Mining Genomes. [[Media:ADRC 2010 genmine (4).ppt|presentation]] (24 slides)<br />
<br />
== Posters ==<br />
* EDRC 2023. What's new: FlyBase updates.<br />
* EDRC 2023. Outreach: FlyBase outreach resources.<br />
* EDRC 2023. FlyCyc: updating the metabolic network for Drosophila melanogaster. [[Media:FlyCyc_EDRC2023_poster.pdf|pdf]]<br />
* ISB 2023. Capturing the experimental research history of signalling pathways in Drosophila melanogaster. [[Media:Pathway-poster-for-ISB2023.pdf|pdf]]<br />
* ISB 2023. FlyCyc: updating the metabolic network for Drosophila melanogaster. [[Media:Marygold_ISB_2023.pdf|pdf]]<br />
* ADRC 2023. Exploiting single-cell RNA-sequencing data in FlyBase. [[Media:ADRC2023_Poster.pdf | pdf]]<br />
* ADRC 2021. Progress towards functional understanding of the gene repertoire of Drosophila. [[Media:Poster_ADRC2021_hattrill-compressed.pdf|pdf]]<br />
**Supplemental table of GO annotation count for protein-coding genes. [[Media:ADRC_2021_understudied_genes.xlsx|xlsx]]<br />
* ADRC 2021. An enzyme catalog for Drosophila melanogaster. [[Media:Marygold_531C_ePoster.pdf|pdf]]<br />
* TAGC 2020. What's new in FlyBase. [[Media:TAGC2020_whats_new.pdf|pdf]]<br />
* EDRC 2019. Systematising knowledge of Drosophila pathway members to fuel biological discovery. [[Media:EDRC2019-Pathways.pdf|pdf]]<br />
* EDRC 2019. What's New in FlyBase. [[Media:EDRC_2019_whats_new.pdf|pdf]]<br />
* ISB 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ISB2019-Pathways.pdf|pdf]]<br />
* ISB 2019. Experimental tools: a new way to categorise transgenic alleles in FlyBase. [[Media:ISB2019_experimental_tools.pdf|pdf]]<br />
* ISB 2019. The Drosophila Anatomy Ontology. [[Media:ISB2019_DAO.pdf|pdf]]<br />
* ADRC 2019. FlyBase: A Valuable Source of Molecular Interaction Data. [[Media:fb_poster.pdf|pdf]]<br />
* ADRC 2019. An evidence-based model for representing signaling pathways in FlyBase. [[Media:ADRC_2019_Pathways.pdf|pdf]]<br />
* ADRC 2019. Finding Human disease models in FlyBase: You can get there from here. [[Media:Disease_Navigation_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Finding GAL4 drivers and other transgenic tools in FlyBase. [[Media:GAL4_and_Tools_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2019. Improving enzyme annotation in FlyBase. [[Media:Enzymes_poster_ADRC2019.pdf|pdf]]<br />
* ADRC 2018. FlyBase 2.0 - What’s new? [[Media:VitorADRC2018-FB_2.0_whatsnew.pdf|pdf]]<br />
* ADRC 2018. FlyBase & Community. [[Media:VitorADRC2018-FBandCommunity.pdf|pdf]]<br />
* ADRC 2018. Functional Annotation of Enzymes in FlyBase. [[Media:Phani_ADRC_2018.pdf|pdf]]<br />
* ADRC 2018. Finding GAL4 Drivers in FlyBase. [[Media:Gramates_GAL4_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. Finding Human Disease Models in FlyBase. [[Media:Gramates_Disease_ADRC2018.pdf|pdf]]<br />
* ADRC 2018. FlyBase: large-scale datasets and single-cell technologies. [[Media:dos_Santos_ADRC2018.pdf|pdf]]<br />
* ISB 2018. FlyBase Representative Publications: using annotation data to identify key papers on a gene. [[Media:ISB-2018-poster-Representative-Publications.pdf|pdf]]<br />
* EDRC 2017. Finding the right tool for the job: new ways to find particular types of transgenic construct in FlyBase. [[Media:EDRC_2017_experimental_tools.pdf|pdf]]<br />
* EDRC 2017. Function-centered approaches for finding and analyzing genes within FlyBase. [[Media:EDRC_poster_function.pdf|pdf]]<br />
* ADRC 2017. FlyBase and Community. [[Media:FBandCommunity.pdf|pdf]]<br />
* ISB 2017. Author Reagent Table: a proposal. [[Media:BioCuration2017_Author_Reagent_Table_Poster.pdf|pdf]]<br />
* ISB 2017. Building a comprehensive catalog of Drosophila datasets at FlyBase. [[Media:BioCuration2017_Datasets_Poster.pdf|pdf]]<br />
* Neurofly 2016. The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2016.pdf|pdf]]<br />
* TAGC/ADRC 2016. Enhanced Orthology Data in FlyBase. [[Media:TAGC_orthologs_poster.pdf|pdf]]<br />
* TAGC/ADRC 2016. FlyBase in the Community. [[Media:2016_TAGC_FBCommunityPoster.pdf|pdf]]<br />
* TAGC/ADRC 2016. Human Disease Model Reports in FlyBase. [[Media:TAGC16_HDMR_poster.pdf|pdf]]<br />
* EDRC 2015. What's New in FlyBase? [[Media: EDRC_2015_poster.pdf|pdf]]<br />
* ADRC 2015. Gene Groups in FlyBase. [[Media:ADRC2015_FlyBase_Gene_Groups.pdf|pdf]]<br />
* Neurofly 2014 P-9, The Drosophila neuroanatomy ontology. [[Media:FlyBasePoster_NeuroFly2014.pdf|pdf]]<br />
* Neurofly 2014 P-169, Representing ''Drosophila'' models of Human Disease in FlyBase. [[Media:Neurofly_2014_human_disease.pdf|pdf]]<br />
* ADRC 2014 767B, FlyBase Gene Model Annotations: Impact of High Throughput Data. [[Media:ADRC2014_poster1.pdf|pdf]]<br />
* ADRC 2014 774C, FlyBase Gene Model Annotations: The Rule-Benders. [[Media:ADRC2014_poster2.pdf|pdf]]<br />
* ADRC 2014, Gene Groups in FlyBase. [[Media:ADRC_GeneGroups.pdf|pdf]]<br />
* ADRC 2014, Human-health-related models in Drosophila melanogaster. [[Media:ADRC_Human_health_related_models.pdf|pdf]]<br />
* ISB 2012. Impact of High Throughput Data on the Drosophila melanogaster Annotation Set. [[Media:Biocurator.2012.pdf|pdf]]<br />
* ADRC 2010. Data in FlyBase (How different types of data are stored and accessed). [[Media:DataInFlyBasePosterADRC2010.pdf|pdf]]<br />
* ADRC 2009. Fast Track Your Paper. [[Media:How to add a paper to FlyBase 2009.pdf|pdf]]<br />
* ADRC 2009. Working with Large Datasets. [[Media:FlyBase Working with Large Data Sets 2009.pdf|pdf]]<br />
<br />
== Pamphlets and Handouts ==<br />
* ADRC 2019. New tools, features, and resources for 2019. [[Media:ADRC2019_NewTools.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. What to Know about FlyBase 2.0, 2018. [[Media:2.0.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2018. FlyBase Feature Focus, 2018. [[Media:FeatureFocus.ADRC2018.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. What's New, 2017. [[Media:Whats_New_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2017. General Information, 2017. [[Media:General_Information_ADRC2017.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. What's New, 2016. [[Media:Whats_New_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2016. General Information, 2016. [[Media:General_Information_TAGC2016.pdf|pamphlet]] (2 pages)<br />
* ADRC 2015. What's New, 2015. [[Media:WhatsnewADRC2015.pdf|pamphlet]] (2 pages)<br />
* ADRC 2014. What's New, 2014. [[Media:WhatsnewADRC2014.pdf|pamphlet]] (2 pages)<br />
* ADRC/EDRC 2013. New and Notable, 2013. [[Media:2013EDRC handout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2012. QuickSearch and GBrowse Redesign, 2012. [[Media:2012ADRCHandout.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. Quick-Start Guide, 2011. [[Media:QuickReference2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2011. New and Notable, 2011. [[Media:NewandNotable2011.pdf|pamphlet]] (2 pages)<br />
* ADRC 2010. New and Notable, 2010. [[Media:NewandNotable2010r2.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. General Information, 2009. [[Media:FlyBase General Information 2009.pdf|pamphlet]] (2 pages)<br />
* ADRC 2009. New and Notable, 2009. [[Media:FlyBase_New_and_Notable_2009.pdf|pamphlet]] (2 pages)<br />
* Cambridge, UK FlyBase workshop 2009. Introduction to FlyBase Workshop [[Media:FlyBase_workshop_2009.pdf|pamphlet]], 2009. (38 pages)<br />
<br />
== Assorted FlyBase Help Presentations ==<br />
<br />
* 2021. Getting Stocks for Gene Lists. [[Media:Getting stocks for gene lists.pdf|pdf]] (15 slides)<br />
<br />
[[Category:DONE]]</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Community_Advisory_Group&diff=172406FlyBase:Community Advisory Group2023-07-28T14:51:12Z<p>Arzu Ozturk Colak: /* Surveys */</p>
<hr />
<div>==What is the FlyBase Community Advisory Group?==<br />
<br />
The FlyBase Community Advisory Group (FCAG) was launched in September 2014 with the aim of '''gaining greater feedback from the community''' about changes in FlyBase. <br />
<br />
You may not know that FlyBase is generated by a team of 32 people, working at Harvard, Indiana, New Mexico and Cambridge Universities. As the members of the FlyBase team work to improve the amount and usefulness of data in FlyBase, numerous questions arise regarding which data are the most important for Drosophila researchers and how we can most usefully present these data on the website. While we do our best to make changes that will be optimal for all Drosophila researchers, we wanted to be able to consult more widely so that we could be sure that our decisions would be helpful for the greatest number of people.<br />
<br />
'''The group consists of members from any lab worldwide that uses FlyBase as part of its research'''. The FCAG member can be the lab head, a postdoc, student, technician or anyone else who uses FlyBase and feels that they could contribute. FlyBase attracts users from a variety of different backgrounds and our members range from frequent FlyBase users to those who use FlyBase only occasionally or who work primarily with another organism.<br />
<br />
Members of the group are sent '''up to 6 surveys a year''' on a variety of different subjects (see the [[FlyBase:Community Advisory Group#Surveys|Surveys]] section below for details of subjects that have been covered so far).<br />
<br />
==Current membership==<br />
<br />
As of 15<sup>th</sup> November 2021 the FlyBase Community Advisory Group comprised '''890 fly researchers''' from '''46 different countries'''. <br />
<br />
[[File:FCAG members nov 2021 min.png|700px|thumb|left]]<br />
{| class="wikitable" style="text-align: center;"<br />
|-<br />
! Country !! Number of members !! Country !! Number of members<br />
|-<br />
| United States || 344 || Nigeria || 6<br />
|-<br />
| United Kingdom || 101 || Austria || 5<br />
|-<br />
| Germany || 66 || Chile || 5<br />
|-<br />
| China || 41 || Taiwan || 5<br />
|-<br />
| India || 39 || Netherlands || 4<br />
|-<br />
| France || 35 || Singapore || 4<br />
|-<br />
| Spain || 31 || Argentina || 3<br />
|-<br />
| Canada || 25 || New Zealland || 3<br />
|-<br />
| Japan || 20 || Norway || 3<br />
|-<br />
| Italy || 17 || Belgium || 2<br />
|-<br />
| Brazil || 13 || Malta || 2<br />
|-<br />
| Sweden || 11 || Pakistan || 2<br />
|-<br />
| Israel || 10 || Thailand || 2<br />
|-<br />
| Korea South || 10 || Ukraine || 2<br />
|-<br />
| Switzerland || 10 || Cyprus || 1<br />
|-<br />
| Australia || 9 || Czech Republic || 1<br />
|-<br />
| Portugal || 9 || Estonia || 1<br />
|-<br />
| Russian Federation || 9 || Lebanon || 2<br />
|-<br />
| Greece || 7 || Panama || 1<br />
|-<br />
| Hungary || 7 || Poland || 1<br />
|-<br />
| Denmark || 6|| South Africa || 1<br />
|-<br />
| Finland || 6 || Uganda || 1<br />
|-<br />
| Mexico || 6 || Turkey || 1<br />
|}<br />
<br />
==Joining the group==<br />
<br />
Every person who uses FlyBase in their research is welcome into our group. Our aim is to have at least a representative from every lab. If you are interested in joining FCAG please go to the [http://{{flybaseorg}}/static/fcag registration form]<br />
<br />
==Updating your details (current members)==<br />
<br />
If you are an existing member of the group and you would like to update your details click [http://{{flybaseorg}}/contact/email here] to go to our contact FlyBase form and choose the subject ‘FlyBase Community Advisory Group’, detailing the changes you would like to make.<br />
<br />
==Surveys==<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
!width="80"|Date<br />
!width="350"|Subject<br />
!width="10"|Responses<br />
! Results<br />
|-<br />
|style="text-align:center;" |July 2023<br />
|<br />
FlyBase Gene Ontology (GO) Survey<br />
|style="text-align:center;" |<br />
142<br />
|<br />
[[File: FlyBase Gene Ontology (GO) Survey.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Feb 2023<br />
|<br />
FlyBase Survey: 'Have you seen this?'<br />
|style="text-align:center;" |<br />
110<br />
|<br />
[[File: FlyBase Survey - Have you seen this.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Nov 2022<br />
|<br />
FlyBase Features for scRNAseq Data<br />
|style="text-align:center;" |<br />
111<br />
|<br />
[[File: FlyBase_Features_for_scRNAseq_Data.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2022<br />
|<br />
FlyBase ''Drosophila'' Metabolic Pathways<br />
|style="text-align:center;" |<br />
199<br />
|<br />
[[File: FB_Metabolic_Pathways.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Aug 2021<br />
|<br />
FlyBase OrthoDB<br />
|style="text-align:center;" |<br />
272<br />
|<br />
[[File: FB_OrthoDB.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2019<br />
|<br />
FlyBase gene summaries<br />
|style="text-align:center;" |<br />
81<br />
|<br />
[[File: FB_Gene_Summaries.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2019<br />
|<br />
FlyBase bulk data files<br />
|style="text-align:center;" |<br />
70<br />
|<br />
[[File: FB_bulk_data_files.pdf]]<br />
|-<br />
|style="text-align:center;" |May 2018<br />
|<br />
FlyBase 2.0<br />
|style="text-align:center;" |<br />
175<br />
|<br />
[[File: FlyBase_2.0.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2018<br />
|<br />
FlyBase Author Reagent Form<br />
|style="text-align:center;" |<br />
22<br />
|<br />
[[File: ART_survey.pdf]]<br />
|-<br />
|style="text-align:center;" |Dec 2017<br />
|<br />
Drosophila template for NCBI dataset submissions<br />
|style="text-align:center;" |<br />
97<br />
|<br />
[[File: FCAG BioSample template.pdf]]<br />
|-<br />
|style="text-align:center;" |Sept 2017<br />
|<br />
Curation of phenotypes induced or modified by chemical treatments or nutritional challenges<br />
|style="text-align:center;" |<br />
118<br />
|<br />
[[File: Chemical_and_nutritional_phenotype_curation.pdf]]<br />
|-<br />
|style="text-align:center;" |Jan 2017<br />
|<br />
GAL4 Search Improvements<br />
|style="text-align:center;" |<br />
157<br />
|<br />
[[File: GAL4 _Search_Improvements_Survey.pdf]]<br />
|-<br />
|style="text-align:center;" |Nov 2016<br />
|<br />
Display of Gene Ontology Annotations<br />
|style="text-align:center;" |<br />
172<br />
|<br />
[[File: Display of Gene Ontology Annotations survey.pdf]]<br />
|-<br />
|style="text-align:center;" |Sept 2016<br />
|<br />
2016 General FlyBase survey<br />
|style="text-align:center;" |<br />
235<br />
|<br />
[[File: 2016 General FlyBase survey.pdf]]<br />
|-<br />
|style="text-align:center;" |July 2016<br />
|<br />
Protein domain graphics/info<br />
|style="text-align:center;" |<br />
208<br />
|<br />
[[File: FCAGwikiProteinDomainSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | Jan 2016<br />
|<br />
Video tutorials<br />
|style="text-align:center;" |<br />
149<br />
|<br />
[[File: FCAGwikiVideoTutorialSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | Oct 2015<br />
|<br />
Predicting the future of fly research<br />
|style="text-align:center;" |<br />
135<br />
|<br />
[[File: FCAG_predicting_the_future.pdf]]<br />
|-<br />
|style="text-align:center;" | July 2015<br />
|<br />
Default tracks on GBrowse<br />
|style="text-align:center;" |<br />
198<br />
|<br />
[[File: GBrowse_default tracks survey results.pdf]]<br />
|-<br />
|style="text-align:center;" | May 2015<br />
|<br />
Complex mutants and transgenic constructs<br />
|style="text-align:center;" |<br />
274<br />
|<br />
[[File: FCAG_construct_survey_full_results.pdf]]<br />
|-<br />
|style="text-align:center;" | Jan 2015 <br />
| <br />
New 'Gene Group' resource<br />
|style="text-align:center;" |<br />
383<br />
|<br />
[[File: FCAG_GeneGroup_survey_results.pdf]]<br />
|-<br />
|style="text-align:center;" | Oct 2014 <br />
| <br />
* How you use FlyBase and how it could be improved<br />
* The automatically generated gene summaries on the gene report<br />
* Receiving updates from FlyBase<br />
|style="text-align:center;" |<br />
454<br />
|<br />
[[File: FCAG_introductory_survey_results.pdf]]<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=File:FlyBase_Gene_Ontology_(GO)_Survey.pdf&diff=172405File:FlyBase Gene Ontology (GO) Survey.pdf2023-07-28T14:37:41Z<p>Arzu Ozturk Colak: </p>
<hr />
<div></div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172210FlyBase:FAQ2023-05-22T16:44:24Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. <br />
<br />
It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172209FlyBase:FAQ2023-05-22T16:42:37Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172208FlyBase:FAQ2023-05-22T16:42:07Z<p>Arzu Ozturk Colak: /* 7. Genome browser (JBrowse and GBrowse) */</p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. It is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172207FlyBase:FAQ2023-05-22T16:41:30Z<p>Arzu Ozturk Colak: /* 7.2. How can I download FASTA sequence from JBrowse? */</p>
<hr />
<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
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! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
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|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
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! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
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! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
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! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial]. Please note that it is currently not possible to download decorated FASTA from JBrowse; however you can download decorated FASTA from the Gene Report of your gene of interest using the "Get Decorated FASTA" button in the "Genomic Location" section (see Question 8.2 for more information).<br />
<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Community_Advisory_Group&diff=172181FlyBase:Community Advisory Group2023-04-03T10:14:39Z<p>Arzu Ozturk Colak: /* Surveys */</p>
<hr />
<div>==What is the FlyBase Community Advisory Group?==<br />
<br />
The FlyBase Community Advisory Group (FCAG) was launched in September 2014 with the aim of '''gaining greater feedback from the community''' about changes in FlyBase. <br />
<br />
You may not know that FlyBase is generated by a team of 32 people, working at Harvard, Indiana, New Mexico and Cambridge Universities. As the members of the FlyBase team work to improve the amount and usefulness of data in FlyBase, numerous questions arise regarding which data are the most important for Drosophila researchers and how we can most usefully present these data on the website. While we do our best to make changes that will be optimal for all Drosophila researchers, we wanted to be able to consult more widely so that we could be sure that our decisions would be helpful for the greatest number of people.<br />
<br />
'''The group consists of members from any lab worldwide that uses FlyBase as part of its research'''. The FCAG member can be the lab head, a postdoc, student, technician or anyone else who uses FlyBase and feels that they could contribute. FlyBase attracts users from a variety of different backgrounds and our members range from frequent FlyBase users to those who use FlyBase only occasionally or who work primarily with another organism.<br />
<br />
Members of the group are sent '''up to 6 surveys a year''' on a variety of different subjects (see the [[FlyBase:Community Advisory Group#Surveys|Surveys]] section below for details of subjects that have been covered so far).<br />
<br />
==Current membership==<br />
<br />
As of 15<sup>th</sup> November 2021 the FlyBase Community Advisory Group comprised '''890 fly researchers''' from '''46 different countries'''. <br />
<br />
[[File:FCAG members nov 2021 min.png|700px|thumb|left]]<br />
{| class="wikitable" style="text-align: center;"<br />
|-<br />
! Country !! Number of members !! Country !! Number of members<br />
|-<br />
| United States || 344 || Nigeria || 6<br />
|-<br />
| United Kingdom || 101 || Austria || 5<br />
|-<br />
| Germany || 66 || Chile || 5<br />
|-<br />
| China || 41 || Taiwan || 5<br />
|-<br />
| India || 39 || Netherlands || 4<br />
|-<br />
| France || 35 || Singapore || 4<br />
|-<br />
| Spain || 31 || Argentina || 3<br />
|-<br />
| Canada || 25 || New Zealland || 3<br />
|-<br />
| Japan || 20 || Norway || 3<br />
|-<br />
| Italy || 17 || Belgium || 2<br />
|-<br />
| Brazil || 13 || Malta || 2<br />
|-<br />
| Sweden || 11 || Pakistan || 2<br />
|-<br />
| Israel || 10 || Thailand || 2<br />
|-<br />
| Korea South || 10 || Ukraine || 2<br />
|-<br />
| Switzerland || 10 || Cyprus || 1<br />
|-<br />
| Australia || 9 || Czech Republic || 1<br />
|-<br />
| Portugal || 9 || Estonia || 1<br />
|-<br />
| Russian Federation || 9 || Lebanon || 2<br />
|-<br />
| Greece || 7 || Panama || 1<br />
|-<br />
| Hungary || 7 || Poland || 1<br />
|-<br />
| Denmark || 6|| South Africa || 1<br />
|-<br />
| Finland || 6 || Uganda || 1<br />
|-<br />
| Mexico || 6 || Turkey || 1<br />
|}<br />
<br />
==Joining the group==<br />
<br />
Every person who uses FlyBase in their research is welcome into our group. Our aim is to have at least a representative from every lab. If you are interested in joining FCAG please go to the [http://{{flybaseorg}}/static/fcag registration form]<br />
<br />
==Updating your details (current members)==<br />
<br />
If you are an existing member of the group and you would like to update your details click [http://{{flybaseorg}}/contact/email here] to go to our contact FlyBase form and choose the subject ‘FlyBase Community Advisory Group’, detailing the changes you would like to make.<br />
<br />
==Surveys==<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Date<br />
! Subject<br />
! Responses<br />
! Results<br />
|-<br />
|style="text-align:center;" |Feb 2023<br />
|<br />
*FlyBase Survey: 'Have you seen this?'<br />
|style="text-align:center;" |<br />
110<br />
|<br />
[[File: FlyBase Survey - Have you seen this.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Nov 2022<br />
|<br />
*FlyBase Features for scRNAseq Data<br />
|style="text-align:center;" |<br />
111<br />
|<br />
[[File: FlyBase_Features_for_scRNAseq_Data.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2022<br />
|<br />
*FlyBase ''Drosophila'' Metabolic Pathways<br />
|style="text-align:center;" |<br />
199<br />
|<br />
[[File: FB_Metabolic_Pathways.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Aug 2021<br />
|<br />
*FlyBase OrthoDB<br />
|style="text-align:center;" |<br />
272<br />
|<br />
[[File: FB_OrthoDB.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2019<br />
|<br />
*FlyBase gene summaries<br />
|style="text-align:center;" |<br />
81<br />
|<br />
[[File: FB_Gene_Summaries.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2019<br />
|<br />
*FlyBase bulk data files<br />
|style="text-align:center;" |<br />
70<br />
|<br />
[[File: FB_bulk_data_files.pdf]]<br />
|-<br />
|style="text-align:center;" |May 2018<br />
|<br />
*FlyBase 2.0<br />
|style="text-align:center;" |<br />
175<br />
|<br />
[[File: FlyBase_2.0.pdf]]<br />
|-<br />
|style="text-align:center;" |February 2018<br />
|<br />
*FlyBase Author Reagent Form<br />
|style="text-align:center;" |<br />
22<br />
|<br />
[[File: ART_survey.pdf]]<br />
|-<br />
|style="text-align:center;" |December 2017<br />
|<br />
*Drosophila template for NCBI dataset submissions<br />
|style="text-align:center;" |<br />
97<br />
|<br />
[[File: FCAG BioSample template.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2017<br />
|<br />
*Curation of phenotypes induced or modified by chemical treatments or nutritional challenges<br />
|style="text-align:center;" |<br />
118<br />
|<br />
[[File: Chemical_and_nutritional_phenotype_curation.pdf]]<br />
|-<br />
|style="text-align:center;" |January 2017<br />
|<br />
*GAL4 Search Improvements<br />
|style="text-align:center;" |<br />
157<br />
|<br />
[[File: GAL4 _Search_Improvements_Survey.pdf]]<br />
|-<br />
|style="text-align:center;" |November 2016<br />
|<br />
*Display of Gene Ontology Annotations<br />
|style="text-align:center;" |<br />
172<br />
|<br />
[[File: Display of Gene Ontology Annotations survey.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2016<br />
|<br />
*2016 General FlyBase survey<br />
|style="text-align:center;" |<br />
235<br />
|<br />
[[File: 2016 General FlyBase survey.pdf]]<br />
|-<br />
|style="text-align:center;" |July 2016<br />
|<br />
*Protein domain graphics/info<br />
|style="text-align:center;" |<br />
208<br />
|<br />
[[File: FCAGwikiProteinDomainSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2016<br />
|<br />
*Video tutorials<br />
|style="text-align:center;" |<br />
149<br />
|<br />
[[File: FCAGwikiVideoTutorialSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2015<br />
|<br />
* Predicting the future of fly research<br />
|style="text-align:center;" |<br />
135<br />
|<br />
[[File: FCAG_predicting_the_future.pdf]]<br />
|-<br />
|style="text-align:center;" | July 2015<br />
|<br />
* Default tracks on GBrowse<br />
|style="text-align:center;" |<br />
198<br />
|<br />
[[File: GBrowse_default tracks survey results.pdf]]<br />
|-<br />
|style="text-align:center;" | May 2015<br />
|<br />
* Complex mutants and transgenic constructs<br />
|style="text-align:center;" |<br />
274<br />
|<br />
[[File: FCAG_construct_survey_full_results.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2015 <br />
| <br />
* New 'Gene Group' resource<br />
|style="text-align:center;" |<br />
383<br />
|<br />
[[File: FCAG_GeneGroup_survey_results.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2014 <br />
| <br />
* How you use FlyBase and how it could be improved<br />
* The automatically generated gene summaries on the gene report<br />
* Receiving updates from FlyBase<br />
|style="text-align:center;" |<br />
454<br />
|<br />
[[File: FCAG_introductory_survey_results.pdf]]<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Community_Advisory_Group&diff=172180FlyBase:Community Advisory Group2023-04-03T09:54:37Z<p>Arzu Ozturk Colak: /* Surveys */</p>
<hr />
<div>==What is the FlyBase Community Advisory Group?==<br />
<br />
The FlyBase Community Advisory Group (FCAG) was launched in September 2014 with the aim of '''gaining greater feedback from the community''' about changes in FlyBase. <br />
<br />
You may not know that FlyBase is generated by a team of 32 people, working at Harvard, Indiana, New Mexico and Cambridge Universities. As the members of the FlyBase team work to improve the amount and usefulness of data in FlyBase, numerous questions arise regarding which data are the most important for Drosophila researchers and how we can most usefully present these data on the website. While we do our best to make changes that will be optimal for all Drosophila researchers, we wanted to be able to consult more widely so that we could be sure that our decisions would be helpful for the greatest number of people.<br />
<br />
'''The group consists of members from any lab worldwide that uses FlyBase as part of its research'''. The FCAG member can be the lab head, a postdoc, student, technician or anyone else who uses FlyBase and feels that they could contribute. FlyBase attracts users from a variety of different backgrounds and our members range from frequent FlyBase users to those who use FlyBase only occasionally or who work primarily with another organism.<br />
<br />
Members of the group are sent '''up to 6 surveys a year''' on a variety of different subjects (see the [[FlyBase:Community Advisory Group#Surveys|Surveys]] section below for details of subjects that have been covered so far).<br />
<br />
==Current membership==<br />
<br />
As of 15<sup>th</sup> November 2021 the FlyBase Community Advisory Group comprised '''890 fly researchers''' from '''46 different countries'''. <br />
<br />
[[File:FCAG members nov 2021 min.png|700px|thumb|left]]<br />
{| class="wikitable" style="text-align: center;"<br />
|-<br />
! Country !! Number of members !! Country !! Number of members<br />
|-<br />
| United States || 344 || Nigeria || 6<br />
|-<br />
| United Kingdom || 101 || Austria || 5<br />
|-<br />
| Germany || 66 || Chile || 5<br />
|-<br />
| China || 41 || Taiwan || 5<br />
|-<br />
| India || 39 || Netherlands || 4<br />
|-<br />
| France || 35 || Singapore || 4<br />
|-<br />
| Spain || 31 || Argentina || 3<br />
|-<br />
| Canada || 25 || New Zealland || 3<br />
|-<br />
| Japan || 20 || Norway || 3<br />
|-<br />
| Italy || 17 || Belgium || 2<br />
|-<br />
| Brazil || 13 || Malta || 2<br />
|-<br />
| Sweden || 11 || Pakistan || 2<br />
|-<br />
| Israel || 10 || Thailand || 2<br />
|-<br />
| Korea South || 10 || Ukraine || 2<br />
|-<br />
| Switzerland || 10 || Cyprus || 1<br />
|-<br />
| Australia || 9 || Czech Republic || 1<br />
|-<br />
| Portugal || 9 || Estonia || 1<br />
|-<br />
| Russian Federation || 9 || Lebanon || 2<br />
|-<br />
| Greece || 7 || Panama || 1<br />
|-<br />
| Hungary || 7 || Poland || 1<br />
|-<br />
| Denmark || 6|| South Africa || 1<br />
|-<br />
| Finland || 6 || Uganda || 1<br />
|-<br />
| Mexico || 6 || Turkey || 1<br />
|}<br />
<br />
==Joining the group==<br />
<br />
Every person who uses FlyBase in their research is welcome into our group. Our aim is to have at least a representative from every lab. If you are interested in joining FCAG please go to the [http://{{flybaseorg}}/static/fcag registration form]<br />
<br />
==Updating your details (current members)==<br />
<br />
If you are an existing member of the group and you would like to update your details click [http://{{flybaseorg}}/contact/email here] to go to our contact FlyBase form and choose the subject ‘FlyBase Community Advisory Group’, detailing the changes you would like to make.<br />
<br />
==Surveys==<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Date<br />
! Subject<br />
! Responses<br />
! Results<br />
|-<br />
|style="text-align:center;" |Feb 2023<br />
|<br />
*FlyBase Survey: "Have you seen this?"<br />
|style="text-align:center;" |<br />
110<br />
|<br />
[[File: FlyBase Survey - Have you seen this.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Nov 2022<br />
|<br />
*FlyBase Features for scRNAseq Data<br />
|style="text-align:center;" |<br />
111<br />
|<br />
[[File: FlyBase_Features_for_scRNAseq_Data.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2022<br />
|<br />
*FlyBase ''Drosophila'' Metabolic Pathways<br />
|style="text-align:center;" |<br />
199<br />
|<br />
[[File: FB_Metabolic_Pathways.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Aug 2021<br />
|<br />
*FlyBase OrthoDB<br />
|style="text-align:center;" |<br />
272<br />
|<br />
[[File: FB_OrthoDB.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2019<br />
|<br />
*FlyBase gene summaries<br />
|style="text-align:center;" |<br />
81<br />
|<br />
[[File: FB_Gene_Summaries.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2019<br />
|<br />
*FlyBase bulk data files<br />
|style="text-align:center;" |<br />
70<br />
|<br />
[[File: FB_bulk_data_files.pdf]]<br />
|-<br />
|style="text-align:center;" |May 2018<br />
|<br />
*FlyBase 2.0<br />
|style="text-align:center;" |<br />
175<br />
|<br />
[[File: FlyBase_2.0.pdf]]<br />
|-<br />
|style="text-align:center;" |February 2018<br />
|<br />
*FlyBase Author Reagent Form<br />
|style="text-align:center;" |<br />
22<br />
|<br />
[[File: ART_survey.pdf]]<br />
|-<br />
|style="text-align:center;" |December 2017<br />
|<br />
*Drosophila template for NCBI dataset submissions<br />
|style="text-align:center;" |<br />
97<br />
|<br />
[[File: FCAG BioSample template.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2017<br />
|<br />
*Curation of phenotypes induced or modified by chemical treatments or nutritional challenges<br />
|style="text-align:center;" |<br />
118<br />
|<br />
[[File: Chemical_and_nutritional_phenotype_curation.pdf]]<br />
|-<br />
|style="text-align:center;" |January 2017<br />
|<br />
*GAL4 Search Improvements<br />
|style="text-align:center;" |<br />
157<br />
|<br />
[[File: GAL4 _Search_Improvements_Survey.pdf]]<br />
|-<br />
|style="text-align:center;" |November 2016<br />
|<br />
*Display of Gene Ontology Annotations<br />
|style="text-align:center;" |<br />
172<br />
|<br />
[[File: Display of Gene Ontology Annotations survey.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2016<br />
|<br />
*2016 General FlyBase survey<br />
|style="text-align:center;" |<br />
235<br />
|<br />
[[File: 2016 General FlyBase survey.pdf]]<br />
|-<br />
|style="text-align:center;" |July 2016<br />
|<br />
*Protein domain graphics/info<br />
|style="text-align:center;" |<br />
208<br />
|<br />
[[File: FCAGwikiProteinDomainSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2016<br />
|<br />
*Video tutorials<br />
|style="text-align:center;" |<br />
149<br />
|<br />
[[File: FCAGwikiVideoTutorialSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2015<br />
|<br />
* Predicting the future of fly research<br />
|style="text-align:center;" |<br />
135<br />
|<br />
[[File: FCAG_predicting_the_future.pdf]]<br />
|-<br />
|style="text-align:center;" | July 2015<br />
|<br />
* Default tracks on GBrowse<br />
|style="text-align:center;" |<br />
198<br />
|<br />
[[File: GBrowse_default tracks survey results.pdf]]<br />
|-<br />
|style="text-align:center;" | May 2015<br />
|<br />
* Complex mutants and transgenic constructs<br />
|style="text-align:center;" |<br />
274<br />
|<br />
[[File: FCAG_construct_survey_full_results.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2015 <br />
| <br />
* New 'Gene Group' resource<br />
|style="text-align:center;" |<br />
383<br />
|<br />
[[File: FCAG_GeneGroup_survey_results.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2014 <br />
| <br />
* How you use FlyBase and how it could be improved<br />
* The automatically generated gene summaries on the gene report<br />
* Receiving updates from FlyBase<br />
|style="text-align:center;" |<br />
454<br />
|<br />
[[File: FCAG_introductory_survey_results.pdf]]<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=File:FlyBase_Survey_-_Have_you_seen_this.pdf&diff=172179File:FlyBase Survey - Have you seen this.pdf2023-04-03T09:50:27Z<p>Arzu Ozturk Colak: </p>
<hr />
<div></div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172153FlyBase:FAQ2023-03-20T10:00:00Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172150FlyBase:FAQ2023-03-14T09:54:42Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. Melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. ''D. Melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. Melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172149FlyBase:FAQ2023-03-13T19:02:02Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''D. Melanogaster'' as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
<br />
== <big>'''2. ''D. Melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. Melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172148FlyBase:FAQ2023-03-13T19:00:34Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Drosophila as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
<br />
== <big>'''2. ''D. Melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. Melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Single-cell RNA-sequencing data</big>''' ==<br />
===15.1. I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase? ===<br />
The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
== '''<big>16. Referencing FlyBase</big>''' ==<br />
===16.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===16.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>17. Stocks</big>''' ==<br />
===17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>18. Submitting data before publication</big>''' ==<br />
===18.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>19. Web server</big>''' ==<br />
===19.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172147FlyBase:FAQ2023-03-13T18:54:20Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Drosophila as a model organism<br />
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! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
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! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Single-cell RNA-sequencing data<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I’ve completed a scRNAseq study that I am about to publish. Is there anything I should do to ensure the dataset reaches FlyBase?<br />
|-<br />
|style="text-align: left"| || The only thing you have to do is to make your raw data files available in a public data store, such as the [https://www.ncbi.nlm.nih.gov/gds/?term= NCBI’s Gene Expression Omnibus] or the [https://www.ebi.ac.uk/biostudies/arrayexpress EMBL-EBI’s ArrayExpress] – something that, as you probably know, is already required anyway by most journals for publishing a study that reports results from high-throughput sequencing methods. Once your paper is published, it will automatically picked up by our scRNAseq curators, who will then contact you to request your cell type annotations if relevant.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 17.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 18.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |19. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 19.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
<br />
== <big>'''2. ''D. Melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. Melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Referencing FlyBase</big>''' ==<br />
===15.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===15.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>16. Stocks</big>''' ==<br />
===16.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===16.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===16.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>17. Submitting data before publication</big>''' ==<br />
===17.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===17.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>18. Web server</big>''' ==<br />
===18.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172146FlyBase:FAQ2023-03-13T18:49:56Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Drosophila as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 16.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
<br />
== <big>'''2. ''D. Melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. Melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Referencing FlyBase</big>''' ==<br />
===15.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===15.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>16. Stocks</big>''' ==<br />
===16.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===16.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===16.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>17. Submitting data before publication</big>''' ==<br />
===17.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===17.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>18. Web server</big>''' ==<br />
===18.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172145FlyBase:FAQ2023-03-13T18:48:30Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Drosophila as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 16.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
<br />
== <big>'''2. ''D. Melanogaster'' as a model organism'''</big> ==<br />
=== 2.1. Where would I find general information about ''D. Melanogaster''? ===<br />
Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
<br />
== <big>'''3. Fast-Track Your Paper'''</big> ==<br />
=== 3.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 3.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 3.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 3.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 3.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 3.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 3.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 3.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''4. FlyBase Community Advisory Group'''</big> ==<br />
=== 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
=== 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? ===<br />
Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
<br />
<br />
== <big>'''5. FlyBase fee'''</big> ==<br />
=== 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>6. FlyBase people database</big>''' ==<br />
=== 6.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>7. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
=== 7.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===7.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>8. Gene data</big>''' ==<br />
=== 8.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 8.2 How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 8.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>9. Gene model and genome annotation</big>''' ==<br />
=== 9.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 9.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===9.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===9.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===9.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===9.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===9.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===9.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===9.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===9.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>10. Gene name/rename</big>''' ==<br />
===10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>11. Job postings</big>''' ==<br />
===11.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>12. Meetings and courses</big>''' ==<br />
===12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>13. Nomenclature</big>''' ==<br />
===13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>14. ''Non-melanogaster'' species</big>''' ==<br />
===14.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>15. Referencing FlyBase</big>''' ==<br />
===15.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===15.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>16. Stocks</big>''' ==<br />
===16.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===16.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===16.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>17. Submitting data before publication</big>''' ==<br />
===17.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===17.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>18. Web server</big>''' ==<br />
===18.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172144FlyBase:FAQ2023-03-13T18:36:29Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Drosophila as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 16.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 6.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 6.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172143FlyBase:FAQ2023-03-13T18:35:09Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Drosophila as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 16.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 6.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 6.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172142FlyBase:FAQ2023-03-13T18:34:25Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
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|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Drosophila as a model organism<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 3.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 3.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 3.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 3.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 3.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 3.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 3.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 3.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 3.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
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! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 4.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 8.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 8.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 8.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 9.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 9.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 9.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 9.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 9.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 9.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 9.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 9.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 9.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 9.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 9.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 9.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 9.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 16.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 16.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |17. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 17.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 17.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |18. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 18.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 6.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 6.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172141FlyBase:FAQ2023-03-13T18:29:26Z<p>Arzu Ozturk Colak: </p>
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<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
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! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Drosophila as a model organism<br />
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! style="text-align: left" | 2.1. !! style="text-align: left" | Where would I find general information about ''D. Melanogaster''?<br />
|-<br />
|style="text-align: left"| || Please check our [https://wiki.flybase.org/wiki/FlyBase:New_to_Flies 'New to Flies' page].<br />
|}<br />
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{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 2.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 2.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 6.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 6.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 14.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 6.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 6.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172140FlyBase:FAQ2023-03-13T18:26:35Z<p>Arzu Ozturk Colak: </p>
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<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 2.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 2.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase Community Advisory Group<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I join the FlyBase Community Advisory Group (FCAG)?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form].<br />
|-<br />
! style="text-align: left" | 3.2. !! style="text-align: left" | I am a current member of the FCAG. I have moved to a new institution, so could you please update my details?<br />
|-<br />
|style="text-align: left"| || Please fill in the [http://flybase.org/static/fcag FCAG registration form], so that we can update your information in our database.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 6.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|-<br />
! style="text-align: left" | 6.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
|-<br />
|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 14.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 6.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 6.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
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{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172139FlyBase:FAQ2023-03-13T18:20:55Z<p>Arzu Ozturk Colak: </p>
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<div>__NOTOC__<br />
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{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
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! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
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! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
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|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
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! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
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! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
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|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
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! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
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|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
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! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
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|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
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! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
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|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
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! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
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|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
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! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
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|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
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! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
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|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
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! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
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|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
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! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
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|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
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! style="text-align: left" | 2.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
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|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
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! style="text-align: left" | 2.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
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|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
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! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
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! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
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|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
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! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
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! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
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|style="text-align: left"| || No, the FlyBase people database was retired.<br />
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! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
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! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
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|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
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! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
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|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
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! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
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! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
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|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
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! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
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|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
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You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
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The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
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! style="text-align: left" | 6.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
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|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
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! style="text-align: left" | 6.4. !! style="text-align: left" | How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms?<br />
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|style="text-align: left"| || You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
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! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
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! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
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|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
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! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
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|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
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! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
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|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
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! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
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|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
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! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
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|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
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! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
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|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
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! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
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|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
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! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
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|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
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! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
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|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
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! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
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|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
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! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
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|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
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! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
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|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
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! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
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|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
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! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
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|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
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''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
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! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
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|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
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! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
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|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
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For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
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If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
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If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
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! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
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! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
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|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
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! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
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! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
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|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
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! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
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! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
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|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
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! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
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! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
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|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
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! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
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! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 14.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 6.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 6.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172138FlyBase:FAQ2023-03-13T18:19:05Z<p>Arzu Ozturk Colak: /* 6. Gene data */</p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 2.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 2.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 6.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 14.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 6.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
=== 6.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? ===<br />
You can find this information on the Transcript Report for your transcript of interest, in a section titled 'cDNA Clones Consistent with Transcript'. You can also visually compare cDNAs and ESTs with your transcript of interest in JBrowse: select all the tracks under the 'Transcript Sequences' subheading, which is under the 'Transcript Level Features' heading.<br />
<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172137FlyBase:FAQ2023-03-13T18:17:16Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 2.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 2.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|-<br />
! style="text-align: left" | 6.3. !! style="text-align: left" | I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how?<br />
|-<br />
|style="text-align: left"| || You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 14.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
=== 6.3. I’ve noticed that a ‘Gene Summary’ for a particular gene seems out-of-date. Can I propose a more up-to-date summary and if so, how? ===<br />
You are welcome to send us a proposed update. You may do so by using [http://flybase.org/contact/email our contact form] and by selecting “Gene Snapshots” as the subject of your message.<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172136FlyBase:FAQ2023-03-13T16:33:55Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 2.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 2.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
|-<br />
! style="text-align: left" | 14.3. !! style="text-align: left" | I got a stock from FlyBase and I found something about that stock that the community should know. What can I do?<br />
|-<br />
|style="text-align: left"| || Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
===14.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? ===<br />
Please send us a personal communication using [http://flybase.org/contact/email the FlyBase contact form]. If your data is indeed relevant for the fly community, it will be added to our report page for that stock.<br />
<br />
Please note that FlyBase does not distribute stocks, we merely provide information about them. If you suspect the stock you obtained is not what you expected (e.g. a different allele than the one requested), you should contact directly the stock center you obtained the stock from. <br />
<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172135FlyBase:FAQ2023-03-13T16:27:14Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|-<br />
! style="text-align: left" | 2.10. !! style="text-align: left" |We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time?<br />
|-<br />
|style="text-align: left"| || We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
|-<br />
! style="text-align: left" | 2.11. !! style="text-align: left" |I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, the FTYP system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here]. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=172134FlyBase:FAQ2023-03-13T16:23:36Z<p>Arzu Ozturk Colak: /* 2. Fast-Track Your Paper */</p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here]. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
=== 2.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time ? ===<br />
We don't send out a confirmation email when you finish submitting your data. Once you have clicked the 'Submit Your Paper' button at the end of the process, you should get a 'Thank You!' screen. So as long as you see this page, then your data has been entered successfully.<br />
=== 2.11. I received an email asking me to submit a FTYP form about my paper, but I completely forgot to do it. Will the results of my paper still be visible on FlyBase? ===<br />
Yes, the “Fast-Track Your Paper” (FTYP) system is intended to speed up the curation process, but if your paper is relevant for FlyBase, it will ultimately be curated even if you did not use FTYP. We would really appreciate it if you do use FTYP for your next papers though, as it saves us valuable curator time.<br />
<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=171974FlyBase:FAQ2022-12-28T14:31:03Z<p>Arzu Ozturk Colak: /* 5.1. Is GBrowse being discontinued? */</p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here]. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] video tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=171973FlyBase:FAQ2022-12-28T14:27:38Z<p>Arzu Ozturk Colak: /* 5.1. Is GBrowse being discontinued? */</p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here]. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries. You can watch [https://www.youtube.com/watch?v=0w6Mbjgx9-E= Using JBrowse on FlyBase] YouTube tutorial for further information.<br />
<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Community_Advisory_Group&diff=171879FlyBase:Community Advisory Group2022-11-23T10:23:40Z<p>Arzu Ozturk Colak: /* Surveys */</p>
<hr />
<div>==What is the FlyBase Community Advisory Group?==<br />
<br />
The FlyBase Community Advisory Group (FCAG) was launched in September 2014 with the aim of '''gaining greater feedback from the community''' about changes in FlyBase. <br />
<br />
You may not know that FlyBase is generated by a team of 32 people, working at Harvard, Indiana, New Mexico and Cambridge Universities. As the members of the FlyBase team work to improve the amount and usefulness of data in FlyBase, numerous questions arise regarding which data are the most important for Drosophila researchers and how we can most usefully present these data on the website. While we do our best to make changes that will be optimal for all Drosophila researchers, we wanted to be able to consult more widely so that we could be sure that our decisions would be helpful for the greatest number of people.<br />
<br />
'''The group consists of members from any lab worldwide that uses FlyBase as part of its research'''. The FCAG member can be the lab head, a postdoc, student, technician or anyone else who uses FlyBase and feels that they could contribute. FlyBase attracts users from a variety of different backgrounds and our members range from frequent FlyBase users to those who use FlyBase only occasionally or who work primarily with another organism.<br />
<br />
Members of the group are sent '''up to 6 surveys a year''' on a variety of different subjects (see the [[FlyBase:Community Advisory Group#Surveys|Surveys]] section below for details of subjects that have been covered so far).<br />
<br />
==Current membership==<br />
<br />
As of 15<sup>th</sup> November 2021 the FlyBase Community Advisory Group comprised '''890 fly researchers''' from '''46 different countries'''. <br />
<br />
[[File:FCAG members nov 2021 min.png|700px|thumb|left]]<br />
{| class="wikitable" style="text-align: center;"<br />
|-<br />
! Country !! Number of members !! Country !! Number of members<br />
|-<br />
| United States || 344 || Nigeria || 6<br />
|-<br />
| United Kingdom || 101 || Austria || 5<br />
|-<br />
| Germany || 66 || Chile || 5<br />
|-<br />
| China || 41 || Taiwan || 5<br />
|-<br />
| India || 39 || Netherlands || 4<br />
|-<br />
| France || 35 || Singapore || 4<br />
|-<br />
| Spain || 31 || Argentina || 3<br />
|-<br />
| Canada || 25 || New Zealland || 3<br />
|-<br />
| Japan || 20 || Norway || 3<br />
|-<br />
| Italy || 17 || Belgium || 2<br />
|-<br />
| Brazil || 13 || Malta || 2<br />
|-<br />
| Sweden || 11 || Pakistan || 2<br />
|-<br />
| Israel || 10 || Thailand || 2<br />
|-<br />
| Korea South || 10 || Ukraine || 2<br />
|-<br />
| Switzerland || 10 || Cyprus || 1<br />
|-<br />
| Australia || 9 || Czech Republic || 1<br />
|-<br />
| Portugal || 9 || Estonia || 1<br />
|-<br />
| Russian Federation || 9 || Lebanon || 2<br />
|-<br />
| Greece || 7 || Panama || 1<br />
|-<br />
| Hungary || 7 || Poland || 1<br />
|-<br />
| Denmark || 6|| South Africa || 1<br />
|-<br />
| Finland || 6 || Uganda || 1<br />
|-<br />
| Mexico || 6 || Turkey || 1<br />
|}<br />
<br />
==Joining the group==<br />
<br />
Every person who uses FlyBase in their research is welcome into our group. Our aim is to have at least a representative from every lab. If you are interested in joining FCAG please go to the [http://{{flybaseorg}}/static/fcag registration form]<br />
<br />
==Updating your details (current members)==<br />
<br />
If you are an existing member of the group and you would like to update your details click [http://{{flybaseorg}}/contact/email here] to go to our contact FlyBase form and choose the subject ‘FlyBase Community Advisory Group’, detailing the changes you would like to make.<br />
<br />
==Surveys==<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Date<br />
! Subject<br />
! Responses<br />
! Results<br />
|-<br />
|style="text-align:center;" |Nov 2022<br />
|<br />
*FlyBase Features for scRNAseq Data<br />
|style="text-align:center;" |<br />
111<br />
|<br />
[[File: FlyBase_Features_for_scRNAseq_Data.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2022<br />
|<br />
*FlyBase ''Drosophila'' Metabolic Pathways<br />
|style="text-align:center;" |<br />
199<br />
|<br />
[[File: FB_Metabolic_Pathways.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Aug 2021<br />
|<br />
*FlyBase OrthoDB<br />
|style="text-align:center;" |<br />
272<br />
|<br />
[[File: FB_OrthoDB.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2019<br />
|<br />
*FlyBase gene summaries<br />
|style="text-align:center;" |<br />
81<br />
|<br />
[[File: FB_Gene_Summaries.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2019<br />
|<br />
*FlyBase bulk data files<br />
|style="text-align:center;" |<br />
70<br />
|<br />
[[File: FB_bulk_data_files.pdf]]<br />
|-<br />
|style="text-align:center;" |May 2018<br />
|<br />
*FlyBase 2.0<br />
|style="text-align:center;" |<br />
175<br />
|<br />
[[File: FlyBase_2.0.pdf]]<br />
|-<br />
|style="text-align:center;" |February 2018<br />
|<br />
*FlyBase Author Reagent Form<br />
|style="text-align:center;" |<br />
22<br />
|<br />
[[File: ART_survey.pdf]]<br />
|-<br />
|style="text-align:center;" |December 2017<br />
|<br />
*Drosophila template for NCBI dataset submissions<br />
|style="text-align:center;" |<br />
97<br />
|<br />
[[File: FCAG BioSample template.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2017<br />
|<br />
*Curation of phenotypes induced or modified by chemical treatments or nutritional challenges<br />
|style="text-align:center;" |<br />
118<br />
|<br />
[[File: Chemical_and_nutritional_phenotype_curation.pdf]]<br />
|-<br />
|style="text-align:center;" |January 2017<br />
|<br />
*GAL4 Search Improvements<br />
|style="text-align:center;" |<br />
157<br />
|<br />
[[File: GAL4 _Search_Improvements_Survey.pdf]]<br />
|-<br />
|style="text-align:center;" |November 2016<br />
|<br />
*Display of Gene Ontology Annotations<br />
|style="text-align:center;" |<br />
172<br />
|<br />
[[File: Display of Gene Ontology Annotations survey.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2016<br />
|<br />
*2016 General FlyBase survey<br />
|style="text-align:center;" |<br />
235<br />
|<br />
[[File: 2016 General FlyBase survey.pdf]]<br />
|-<br />
|style="text-align:center;" |July 2016<br />
|<br />
*Protein domain graphics/info<br />
|style="text-align:center;" |<br />
208<br />
|<br />
[[File: FCAGwikiProteinDomainSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2016<br />
|<br />
*Video tutorials<br />
|style="text-align:center;" |<br />
149<br />
|<br />
[[File: FCAGwikiVideoTutorialSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2015<br />
|<br />
* Predicting the future of fly research<br />
|style="text-align:center;" |<br />
135<br />
|<br />
[[File: FCAG_predicting_the_future.pdf]]<br />
|-<br />
|style="text-align:center;" | July 2015<br />
|<br />
* Default tracks on GBrowse<br />
|style="text-align:center;" |<br />
198<br />
|<br />
[[File: GBrowse_default tracks survey results.pdf]]<br />
|-<br />
|style="text-align:center;" | May 2015<br />
|<br />
* Complex mutants and transgenic constructs<br />
|style="text-align:center;" |<br />
274<br />
|<br />
[[File: FCAG_construct_survey_full_results.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2015 <br />
| <br />
* New 'Gene Group' resource<br />
|style="text-align:center;" |<br />
383<br />
|<br />
[[File: FCAG_GeneGroup_survey_results.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2014 <br />
| <br />
* How you use FlyBase and how it could be improved<br />
* The automatically generated gene summaries on the gene report<br />
* Receiving updates from FlyBase<br />
|style="text-align:center;" |<br />
454<br />
|<br />
[[File: FCAG_introductory_survey_results.pdf]]<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Community_Advisory_Group&diff=171878FlyBase:Community Advisory Group2022-11-23T10:23:28Z<p>Arzu Ozturk Colak: /* Surveys */</p>
<hr />
<div>==What is the FlyBase Community Advisory Group?==<br />
<br />
The FlyBase Community Advisory Group (FCAG) was launched in September 2014 with the aim of '''gaining greater feedback from the community''' about changes in FlyBase. <br />
<br />
You may not know that FlyBase is generated by a team of 32 people, working at Harvard, Indiana, New Mexico and Cambridge Universities. As the members of the FlyBase team work to improve the amount and usefulness of data in FlyBase, numerous questions arise regarding which data are the most important for Drosophila researchers and how we can most usefully present these data on the website. While we do our best to make changes that will be optimal for all Drosophila researchers, we wanted to be able to consult more widely so that we could be sure that our decisions would be helpful for the greatest number of people.<br />
<br />
'''The group consists of members from any lab worldwide that uses FlyBase as part of its research'''. The FCAG member can be the lab head, a postdoc, student, technician or anyone else who uses FlyBase and feels that they could contribute. FlyBase attracts users from a variety of different backgrounds and our members range from frequent FlyBase users to those who use FlyBase only occasionally or who work primarily with another organism.<br />
<br />
Members of the group are sent '''up to 6 surveys a year''' on a variety of different subjects (see the [[FlyBase:Community Advisory Group#Surveys|Surveys]] section below for details of subjects that have been covered so far).<br />
<br />
==Current membership==<br />
<br />
As of 15<sup>th</sup> November 2021 the FlyBase Community Advisory Group comprised '''890 fly researchers''' from '''46 different countries'''. <br />
<br />
[[File:FCAG members nov 2021 min.png|700px|thumb|left]]<br />
{| class="wikitable" style="text-align: center;"<br />
|-<br />
! Country !! Number of members !! Country !! Number of members<br />
|-<br />
| United States || 344 || Nigeria || 6<br />
|-<br />
| United Kingdom || 101 || Austria || 5<br />
|-<br />
| Germany || 66 || Chile || 5<br />
|-<br />
| China || 41 || Taiwan || 5<br />
|-<br />
| India || 39 || Netherlands || 4<br />
|-<br />
| France || 35 || Singapore || 4<br />
|-<br />
| Spain || 31 || Argentina || 3<br />
|-<br />
| Canada || 25 || New Zealland || 3<br />
|-<br />
| Japan || 20 || Norway || 3<br />
|-<br />
| Italy || 17 || Belgium || 2<br />
|-<br />
| Brazil || 13 || Malta || 2<br />
|-<br />
| Sweden || 11 || Pakistan || 2<br />
|-<br />
| Israel || 10 || Thailand || 2<br />
|-<br />
| Korea South || 10 || Ukraine || 2<br />
|-<br />
| Switzerland || 10 || Cyprus || 1<br />
|-<br />
| Australia || 9 || Czech Republic || 1<br />
|-<br />
| Portugal || 9 || Estonia || 1<br />
|-<br />
| Russian Federation || 9 || Lebanon || 2<br />
|-<br />
| Greece || 7 || Panama || 1<br />
|-<br />
| Hungary || 7 || Poland || 1<br />
|-<br />
| Denmark || 6|| South Africa || 1<br />
|-<br />
| Finland || 6 || Uganda || 1<br />
|-<br />
| Mexico || 6 || Turkey || 1<br />
|}<br />
<br />
==Joining the group==<br />
<br />
Every person who uses FlyBase in their research is welcome into our group. Our aim is to have at least a representative from every lab. If you are interested in joining FCAG please go to the [http://{{flybaseorg}}/static/fcag registration form]<br />
<br />
==Updating your details (current members)==<br />
<br />
If you are an existing member of the group and you would like to update your details click [http://{{flybaseorg}}/contact/email here] to go to our contact FlyBase form and choose the subject ‘FlyBase Community Advisory Group’, detailing the changes you would like to make.<br />
<br />
==Surveys==<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Date<br />
! Subject<br />
! Responses<br />
! Results<br />
|-<br />
|style="text-align:center;" |Nov 2022<br />
|<br />
*FlyBase Features for scRNAseq Data<br />
|style="text-align:center;" |<br />
111<br />
|<br />
[[File: FlyBase_Features_for_scRNAseq_Data.pdf.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2022<br />
|<br />
*FlyBase ''Drosophila'' Metabolic Pathways<br />
|style="text-align:center;" |<br />
199<br />
|<br />
[[File: FB_Metabolic_Pathways.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Aug 2021<br />
|<br />
*FlyBase OrthoDB<br />
|style="text-align:center;" |<br />
272<br />
|<br />
[[File: FB_OrthoDB.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2019<br />
|<br />
*FlyBase gene summaries<br />
|style="text-align:center;" |<br />
81<br />
|<br />
[[File: FB_Gene_Summaries.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2019<br />
|<br />
*FlyBase bulk data files<br />
|style="text-align:center;" |<br />
70<br />
|<br />
[[File: FB_bulk_data_files.pdf]]<br />
|-<br />
|style="text-align:center;" |May 2018<br />
|<br />
*FlyBase 2.0<br />
|style="text-align:center;" |<br />
175<br />
|<br />
[[File: FlyBase_2.0.pdf]]<br />
|-<br />
|style="text-align:center;" |February 2018<br />
|<br />
*FlyBase Author Reagent Form<br />
|style="text-align:center;" |<br />
22<br />
|<br />
[[File: ART_survey.pdf]]<br />
|-<br />
|style="text-align:center;" |December 2017<br />
|<br />
*Drosophila template for NCBI dataset submissions<br />
|style="text-align:center;" |<br />
97<br />
|<br />
[[File: FCAG BioSample template.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2017<br />
|<br />
*Curation of phenotypes induced or modified by chemical treatments or nutritional challenges<br />
|style="text-align:center;" |<br />
118<br />
|<br />
[[File: Chemical_and_nutritional_phenotype_curation.pdf]]<br />
|-<br />
|style="text-align:center;" |January 2017<br />
|<br />
*GAL4 Search Improvements<br />
|style="text-align:center;" |<br />
157<br />
|<br />
[[File: GAL4 _Search_Improvements_Survey.pdf]]<br />
|-<br />
|style="text-align:center;" |November 2016<br />
|<br />
*Display of Gene Ontology Annotations<br />
|style="text-align:center;" |<br />
172<br />
|<br />
[[File: Display of Gene Ontology Annotations survey.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2016<br />
|<br />
*2016 General FlyBase survey<br />
|style="text-align:center;" |<br />
235<br />
|<br />
[[File: 2016 General FlyBase survey.pdf]]<br />
|-<br />
|style="text-align:center;" |July 2016<br />
|<br />
*Protein domain graphics/info<br />
|style="text-align:center;" |<br />
208<br />
|<br />
[[File: FCAGwikiProteinDomainSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2016<br />
|<br />
*Video tutorials<br />
|style="text-align:center;" |<br />
149<br />
|<br />
[[File: FCAGwikiVideoTutorialSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2015<br />
|<br />
* Predicting the future of fly research<br />
|style="text-align:center;" |<br />
135<br />
|<br />
[[File: FCAG_predicting_the_future.pdf]]<br />
|-<br />
|style="text-align:center;" | July 2015<br />
|<br />
* Default tracks on GBrowse<br />
|style="text-align:center;" |<br />
198<br />
|<br />
[[File: GBrowse_default tracks survey results.pdf]]<br />
|-<br />
|style="text-align:center;" | May 2015<br />
|<br />
* Complex mutants and transgenic constructs<br />
|style="text-align:center;" |<br />
274<br />
|<br />
[[File: FCAG_construct_survey_full_results.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2015 <br />
| <br />
* New 'Gene Group' resource<br />
|style="text-align:center;" |<br />
383<br />
|<br />
[[File: FCAG_GeneGroup_survey_results.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2014 <br />
| <br />
* How you use FlyBase and how it could be improved<br />
* The automatically generated gene summaries on the gene report<br />
* Receiving updates from FlyBase<br />
|style="text-align:center;" |<br />
454<br />
|<br />
[[File: FCAG_introductory_survey_results.pdf]]<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=File:FlyBase_Features_for_scRNAseq_Data.pdf&diff=171877File:FlyBase Features for scRNAseq Data.pdf2022-11-23T10:22:38Z<p>Arzu Ozturk Colak: </p>
<hr />
<div></div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:Community_Advisory_Group&diff=171876FlyBase:Community Advisory Group2022-11-23T10:20:46Z<p>Arzu Ozturk Colak: /* Surveys */</p>
<hr />
<div>==What is the FlyBase Community Advisory Group?==<br />
<br />
The FlyBase Community Advisory Group (FCAG) was launched in September 2014 with the aim of '''gaining greater feedback from the community''' about changes in FlyBase. <br />
<br />
You may not know that FlyBase is generated by a team of 32 people, working at Harvard, Indiana, New Mexico and Cambridge Universities. As the members of the FlyBase team work to improve the amount and usefulness of data in FlyBase, numerous questions arise regarding which data are the most important for Drosophila researchers and how we can most usefully present these data on the website. While we do our best to make changes that will be optimal for all Drosophila researchers, we wanted to be able to consult more widely so that we could be sure that our decisions would be helpful for the greatest number of people.<br />
<br />
'''The group consists of members from any lab worldwide that uses FlyBase as part of its research'''. The FCAG member can be the lab head, a postdoc, student, technician or anyone else who uses FlyBase and feels that they could contribute. FlyBase attracts users from a variety of different backgrounds and our members range from frequent FlyBase users to those who use FlyBase only occasionally or who work primarily with another organism.<br />
<br />
Members of the group are sent '''up to 6 surveys a year''' on a variety of different subjects (see the [[FlyBase:Community Advisory Group#Surveys|Surveys]] section below for details of subjects that have been covered so far).<br />
<br />
==Current membership==<br />
<br />
As of 15<sup>th</sup> November 2021 the FlyBase Community Advisory Group comprised '''890 fly researchers''' from '''46 different countries'''. <br />
<br />
[[File:FCAG members nov 2021 min.png|700px|thumb|left]]<br />
{| class="wikitable" style="text-align: center;"<br />
|-<br />
! Country !! Number of members !! Country !! Number of members<br />
|-<br />
| United States || 344 || Nigeria || 6<br />
|-<br />
| United Kingdom || 101 || Austria || 5<br />
|-<br />
| Germany || 66 || Chile || 5<br />
|-<br />
| China || 41 || Taiwan || 5<br />
|-<br />
| India || 39 || Netherlands || 4<br />
|-<br />
| France || 35 || Singapore || 4<br />
|-<br />
| Spain || 31 || Argentina || 3<br />
|-<br />
| Canada || 25 || New Zealland || 3<br />
|-<br />
| Japan || 20 || Norway || 3<br />
|-<br />
| Italy || 17 || Belgium || 2<br />
|-<br />
| Brazil || 13 || Malta || 2<br />
|-<br />
| Sweden || 11 || Pakistan || 2<br />
|-<br />
| Israel || 10 || Thailand || 2<br />
|-<br />
| Korea South || 10 || Ukraine || 2<br />
|-<br />
| Switzerland || 10 || Cyprus || 1<br />
|-<br />
| Australia || 9 || Czech Republic || 1<br />
|-<br />
| Portugal || 9 || Estonia || 1<br />
|-<br />
| Russian Federation || 9 || Lebanon || 2<br />
|-<br />
| Greece || 7 || Panama || 1<br />
|-<br />
| Hungary || 7 || Poland || 1<br />
|-<br />
| Denmark || 6|| South Africa || 1<br />
|-<br />
| Finland || 6 || Uganda || 1<br />
|-<br />
| Mexico || 6 || Turkey || 1<br />
|}<br />
<br />
==Joining the group==<br />
<br />
Every person who uses FlyBase in their research is welcome into our group. Our aim is to have at least a representative from every lab. If you are interested in joining FCAG please go to the [http://{{flybaseorg}}/static/fcag registration form]<br />
<br />
==Updating your details (current members)==<br />
<br />
If you are an existing member of the group and you would like to update your details click [http://{{flybaseorg}}/contact/email here] to go to our contact FlyBase form and choose the subject ‘FlyBase Community Advisory Group’, detailing the changes you would like to make.<br />
<br />
==Surveys==<br />
<br />
{| class="wikitable" border="1"<br />
|-<br />
! Date<br />
! Subject<br />
! Responses<br />
! Results<br />
|-<br />
|style="text-align:center;" |Nov 2022<br />
|<br />
*FlyBase Features for scRNAseq Data<br />
|style="text-align:center;" |<br />
111<br />
|<br />
[[File: FB_Metabolic_Pathways.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2022<br />
|<br />
*FlyBase ''Drosophila'' Metabolic Pathways<br />
|style="text-align:center;" |<br />
199<br />
|<br />
[[File: FB_Metabolic_Pathways.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Aug 2021<br />
|<br />
*FlyBase OrthoDB<br />
|style="text-align:center;" |<br />
272<br />
|<br />
[[File: FB_OrthoDB.pdf]]<br />
|-<br />
|-<br />
|style="text-align:center;" |Sep 2019<br />
|<br />
*FlyBase gene summaries<br />
|style="text-align:center;" |<br />
81<br />
|<br />
[[File: FB_Gene_Summaries.pdf]]<br />
|-<br />
|style="text-align:center;" |Feb 2019<br />
|<br />
*FlyBase bulk data files<br />
|style="text-align:center;" |<br />
70<br />
|<br />
[[File: FB_bulk_data_files.pdf]]<br />
|-<br />
|style="text-align:center;" |May 2018<br />
|<br />
*FlyBase 2.0<br />
|style="text-align:center;" |<br />
175<br />
|<br />
[[File: FlyBase_2.0.pdf]]<br />
|-<br />
|style="text-align:center;" |February 2018<br />
|<br />
*FlyBase Author Reagent Form<br />
|style="text-align:center;" |<br />
22<br />
|<br />
[[File: ART_survey.pdf]]<br />
|-<br />
|style="text-align:center;" |December 2017<br />
|<br />
*Drosophila template for NCBI dataset submissions<br />
|style="text-align:center;" |<br />
97<br />
|<br />
[[File: FCAG BioSample template.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2017<br />
|<br />
*Curation of phenotypes induced or modified by chemical treatments or nutritional challenges<br />
|style="text-align:center;" |<br />
118<br />
|<br />
[[File: Chemical_and_nutritional_phenotype_curation.pdf]]<br />
|-<br />
|style="text-align:center;" |January 2017<br />
|<br />
*GAL4 Search Improvements<br />
|style="text-align:center;" |<br />
157<br />
|<br />
[[File: GAL4 _Search_Improvements_Survey.pdf]]<br />
|-<br />
|style="text-align:center;" |November 2016<br />
|<br />
*Display of Gene Ontology Annotations<br />
|style="text-align:center;" |<br />
172<br />
|<br />
[[File: Display of Gene Ontology Annotations survey.pdf]]<br />
|-<br />
|style="text-align:center;" |September 2016<br />
|<br />
*2016 General FlyBase survey<br />
|style="text-align:center;" |<br />
235<br />
|<br />
[[File: 2016 General FlyBase survey.pdf]]<br />
|-<br />
|style="text-align:center;" |July 2016<br />
|<br />
*Protein domain graphics/info<br />
|style="text-align:center;" |<br />
208<br />
|<br />
[[File: FCAGwikiProteinDomainSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2016<br />
|<br />
*Video tutorials<br />
|style="text-align:center;" |<br />
149<br />
|<br />
[[File: FCAGwikiVideoTutorialSurvey.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2015<br />
|<br />
* Predicting the future of fly research<br />
|style="text-align:center;" |<br />
135<br />
|<br />
[[File: FCAG_predicting_the_future.pdf]]<br />
|-<br />
|style="text-align:center;" | July 2015<br />
|<br />
* Default tracks on GBrowse<br />
|style="text-align:center;" |<br />
198<br />
|<br />
[[File: GBrowse_default tracks survey results.pdf]]<br />
|-<br />
|style="text-align:center;" | May 2015<br />
|<br />
* Complex mutants and transgenic constructs<br />
|style="text-align:center;" |<br />
274<br />
|<br />
[[File: FCAG_construct_survey_full_results.pdf]]<br />
|-<br />
|style="text-align:center;" | January 2015 <br />
| <br />
* New 'Gene Group' resource<br />
|style="text-align:center;" |<br />
383<br />
|<br />
[[File: FCAG_GeneGroup_survey_results.pdf]]<br />
|-<br />
|style="text-align:center;" | October 2014 <br />
| <br />
* How you use FlyBase and how it could be improved<br />
* The automatically generated gene summaries on the gene report<br />
* Receiving updates from FlyBase<br />
|style="text-align:center;" |<br />
454<br />
|<br />
[[File: FCAG_introductory_survey_results.pdf]]<br />
|}</div>Arzu Ozturk Colakhttps://wiki.flybase.org/mediawiki/index.php?title=FlyBase:FAQ&diff=171874FlyBase:FAQ2022-11-22T14:50:48Z<p>Arzu Ozturk Colak: </p>
<hr />
<div>__NOTOC__<br />
<br />
{| class="wikitable outercollapse" style="width: 100%"<br />
! style="text-align: left; background: #C8C8CD" | <big>FlyBase FAQ</big><br />
|-<br />
| <br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |1. !! style="text-align: left; background: #C8C8CD; width: 100%" | Bulk data retrieval<br />
|-<br />
! style="text-align: left" | 1.1. !! style="text-align: left" |What sort of bulk data files do you offer?<br />
|-<br />
|style="text-align: left"| || The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |2. !! style="text-align: left; background: #C8C8CD; width: 100%" | Fast-Track Your Paper<br />
|-<br />
! style="text-align: left" | 2.1. !! style="text-align: left" |I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.<br />
|-<br />
|style="text-align: left"| || It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
|-<br />
! style="text-align: left" | 2.2. !! style="text-align: left" | For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"?<br />
|-<br />
|style="text-align: left"| || If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
|-<br />
! style="text-align: left" | 2.3. !! style="text-align: left" |I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool.<br />
|-<br />
|style="text-align: left"| || If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
|-<br />
! style="text-align: left" | 2.4. !! style="text-align: left" |I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'?<br />
|-<br />
|style="text-align: left"| || Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
|-<br />
! style="text-align: left" | 2.5. !! style="text-align: left" |I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports?<br />
|-<br />
|style="text-align: left"| || We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
|-<br />
! style="text-align: left" | 2.6. !! style="text-align: left" |I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do?<br />
|-<br />
|style="text-align: left"| || The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action. <br />
|-<br />
! style="text-align: left" | 2.7. !! style="text-align: left" |I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP?<br />
|-<br />
|style="text-align: left"| || No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
|-<br />
! style="text-align: left" | 2.8. !! style="text-align: left" |I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed?<br />
|-<br />
|style="text-align: left"| || If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
|-<br />
! style="text-align: left" | 2.9. !! style="text-align: left" |I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from?<br />
|-<br />
|style="text-align: left"| || Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |3. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase fee<br />
|-<br />
! style="text-align: left" | 3.1. !! style="text-align: left" | How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company?<br />
|-<br />
|style="text-align: left"| || You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |4. !! style="text-align: left; background: #C8C8CD; width: 100%" | FlyBase people database<br />
|-<br />
! style="text-align: left" | 4.1. !! style="text-align: left" | Is FlyBase people database still active?<br />
|-<br />
|style="text-align: left"| || No, the FlyBase people database was retired.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD |5. !! style="text-align: left; background: #C8C8CD; width: 100%" | Genome browser (JBrowse and GBrowse)<br />
|-<br />
! style="text-align: left" | 5.1. !! style="text-align: left" | Is GBrowse being discontinued?<br />
|-<br />
|style="text-align: left"| || Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
|-<br />
! style="text-align: left" | 5.2. !! style="text-align: left" | How can I download FASTA sequence from JBrowse?<br />
|-<br />
|style="text-align: left"| || Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
|}<br />
<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |6. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene data<br />
|-<br />
! style="text-align: left" | 6.1. !! style="text-align: left" | How can I find transgenic constructs with particular characteristics?<br />
|-<br />
|style="text-align: left"| || Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
|-<br />
! style="text-align: left" | 6.2. !! style="text-align: left" | How can I obtain flanking gene sequence?<br />
|-<br />
|style="text-align: left"| || To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |7. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene model and genome annotation<br />
|-<br />
! style="text-align: left" | 7.1. !! style="text-align: left" | What happened to my gene? Its gene report says it is withdrawn.<br />
|-<br />
|style="text-align: left"| || Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
|-<br />
! style="text-align: left" | 7.2. !! style="text-align: left" | I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option.<br />
|-<br />
|style="text-align: left"| || The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
|-<br />
! style="text-align: left" | 7.3. !! style="text-align: left" | I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency?<br />
|-<br />
|style="text-align: left"| || You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
|-<br />
! style="text-align: left" | 7.4. !! style="text-align: left" | These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be?<br />
|-<br />
|style="text-align: left"| || You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.5. !! style="text-align: left" | Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake?<br />
|-<br />
|style="text-align: left"| || You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.6. !! style="text-align: left" | The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon.<br />
|-<br />
|style="text-align: left"| || There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
|-<br />
! style="text-align: left" | 7.7. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
|-<br />
! style="text-align: left" | 7.8. !! style="text-align: left" | What reference genome assemblies have been produced for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || ''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
|-<br />
! style="text-align: left" | 7.9. !! style="text-align: left" | How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? <br />
|-<br />
|style="text-align: left"| || An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
|-<br />
! style="text-align: left" | 7.10. !! style="text-align: left" | How can I submit a correction to the genomic sequence of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
|-<br />
! style="text-align: left" | 7.11. !! style="text-align: left" | How can I submit a correction to a gene model of ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
|-<br />
! style="text-align: left" | 7.12. !! style="text-align: left" | How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
|-<br />
! style="text-align: left" | 7.13. !! style="text-align: left" | Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate?<br />
|-<br />
|style="text-align: left"| || For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
|-<br />
! style="text-align: left" | 7.14. !! style="text-align: left" | What does the annotation release number mean?<br />
|-<br />
|style="text-align: left"| || BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
|-<br />
! style="text-align: left" | 7.15. !! style="text-align: left" | How do I convert coordinates from one genome release to another?<br />
|-<br />
|style="text-align: left"| || You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
|-<br />
! style="text-align: left" | 7.16. !! style="text-align: left" | How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''?<br />
|-<br />
|style="text-align: left"| || New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |8. !! style="text-align: left; background: #C8C8CD; width: 100%" | Gene name/rename<br />
|-<br />
! style="text-align: left" | 8.1. !! style="text-align: left" | When (under what circumstances) does FlyBase consider changing a designated gene name?<br />
|-<br />
|style="text-align: left"| || We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |9. !! style="text-align: left; background: #C8C8CD; width: 100%" | Job postings<br />
|-<br />
! style="text-align: left" | 9.1. !! style="text-align: left" | I want to post a job on FlyBase; how can I do that?<br />
|-<br />
|style="text-align: left"| || You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |10. !! style="text-align: left; background: #C8C8CD; width: 100%" | Meetings or courses<br />
|-<br />
! style="text-align: left" | 10.1. !! style="text-align: left" | I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?<br />
|-<br />
|style="text-align: left"| || Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |11. !! style="text-align: left; background: #C8C8CD; width: 100%" | Nomenclature<br />
|-<br />
! style="text-align: left" | 11.1. !! style="text-align: left" | I identified a gene and would like to name it. Are there any FlyBase guidelines for this?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |12. !! style="text-align: left; background: #C8C8CD; width: 100%" | ''Non-melanogaster'' species<br />
|-<br />
! style="text-align: left" | 12.1. !! style="text-align: left" | I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information?<br />
|-<br />
|style="text-align: left"| || FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |13. !! style="text-align: left; background: #C8C8CD; width: 100%" | Referencing FlyBase<br />
|-<br />
! style="text-align: left" | 13.1. !! style="text-align: left" | Can I use the FlyBase logo in my publication/poster?<br />
|-<br />
|style="text-align: left"| || The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|-<br />
! style="text-align: left" | 13.2. !! style="text-align: left" | I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow?<br />
|-<br />
|style="text-align: left"| || Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |14. !! style="text-align: left; background: #C8C8CD; width: 100%" | Stocks<br />
|-<br />
! style="text-align: left" | 14.1. !! style="text-align: left" | I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this?<br />
|-<br />
|style="text-align: left"| || Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
|-<br />
! style="text-align: left" | 14.2. !! style="text-align: left" | How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase?<br />
|-<br />
|style="text-align: left"| || FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here]. <br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |15. !! style="text-align: left; background: #C8C8CD; width: 100%" | Submitting data before publication<br />
|-<br />
! style="text-align: left" | 15.1. !! style="text-align: left" | I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase?<br />
|-<br />
|style="text-align: left"| || If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
|-<br />
! style="text-align: left" | 15.2. !! style="text-align: left" | I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase?<br />
|-<br />
|style="text-align: left"| || Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
|}<br />
{| class="mw-collapsible mw-collapsed wikitable"<br />
! style="text-align: left; background: #C8C8CD" |16. !! style="text-align: left; background: #C8C8CD; width: 100%" | Web server<br />
|-<br />
! style="text-align: left" | 16.1. !! style="text-align: left" | How do I access data from an older release that is not available via an active archive server?<br />
|-<br />
|style="text-align: left"| || All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
|}<br />
<br />
== <big>'''1. Bulk data retrieval'''</big> ==<br />
=== 1.1. What sort of bulk data files do you offer? ===<br />
The data sets available are described on the [https://wiki.flybase.org/wiki/FlyBase:Downloads_Overview Downloads Overview page].<br />
== <big>'''2. Fast-Track Your Paper'''</big> ==<br />
=== 2.1. I was contacted by FlyBase about my publication. I don't think it is relevant since I didn't investigate any ''Drosophila melanogaster'' genes.===<br />
It is helpful to FlyBase curators to know that your paper has no FlyBase-curatable data; this gives us more time to devote to data-rich papers. The Fast-Track Your Paper tool allows you to quickly indicate that your paper has no curatable data types or investigates no ''Drosophila melanogaster'' genes. <br />
=== 2.2. For "new transgene" under "Drosophila reagents", I constructed a plasmid containing an existing known ''D. melanogaster'' gene. Is this considered as a "new transgene"? ===<br />
If you went on to use the plasmid in vivo (e.g. injected a UAS-geneX construct into ''Drosophila melanogaster'') then this would be considered a new transgene. If you used the plasmid only in cultured cells or in vitro, we do not consider it a new transgene. Please find futher information about FTYP tool [https://wiki.flybase.org/wiki/FlyBase:Fast-Track_Your_Paper here].<br />
=== 2.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. ===<br />
If it is a very recent paper, it may not have entered our bibliography. This means the paper is not available to the Fast Track Your Paper tool yet. Please try again in one or two weeks.<br />
=== 2.4. I was asked to complete the FTYP form for my paper published recently. The paper describes many genes, but it's actually a review article and there is no original data. Should I still list up genes described in this paper as genes that were 'studied'? ===<br />
Any gene you associate with your review will result in your review appearing on the reference list of that gene report. So, we encourage you add any gene(s) that are the focus of your review.<br />
=== 2.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? ===<br />
We only update the public web pages every two months, so depending on when you submit the Fast-Track information, it can take between 3-12 weeks for the reference to appear on gene reports.<br />
=== 2.6. I received a link to Fast-Track our paper but when I go to the link it shows that the paper has been already curated. What should I do? ===<br />
The reason that that link is no longer available is because your paper has already been curated by a FlyBase curator or by another Fast-Track contributor. You don't need to take any further action.<br />
=== 2.7. I have used some genetic reagents but I have not investigated their roles in my paper. I just used them as tools (e.g. selectable marker in crosses, GAL4 driver, FLP to induce clones). Shall I mention these genes in the field "gene studied" of FTYP? ===<br />
No, we are only interested in the genes that you studied (e.g. to analyse their role in development, to determine the mutant phenotype, or to determine where they are expressed), so there is no need to add genes for genetic reagents used as tools.<br />
=== 2.8. I submitted the information to Fast-Track our recent manuscript in which we made a new transgene expressing a human gene. However, when selecting genes studied, the system did not give me the option to select the corresponding human gene. How shall I proceed? ===<br />
If you have made the first reported transgenic construct of a human gene in flies, there will not yet be a FlyBase gene report for that gene. In the Data section (before gene selection), make sure the box for 'New transgene' has been selected, and a FlyBase curator will attach that gene (and the construct) to your paper, after making the appropriate gene report.<br />
=== 2.9. I would like to use Fast-Track for our paper but the email request has gone to another author. Can I still fill in the FTYP from? ===<br />
Yes, you can use the original link that was provided in the email and then change the email address to your own manually in the 'Contact' step.<br />
== <big>'''3. FlyBase fee'''</big> ==<br />
=== 3.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? ===<br />
You can pay the FlyBase fee at [https://secure.touchnet.net/C20832_ustores/web/store_main.jsp?STOREID=117&SINGLESTORE=true this link]. We also have a dedicated [https://wiki.flybase.org/wiki/FlyBase:FlyBase_Website_Access_Fee_FAQ FlyBase Fees FAQ]. Please [mailto:flybase-fees@morgan.harvard.edu contact us] to discuss institutional/departmental/corporate fees.<br />
== '''<big>4. FlyBase people database</big>''' ==<br />
=== 4.1. Is FlyBase people database still active?===<br />
No, the FlyBase people database was retired.<br />
== '''<big>5. Genome browser (JBrowse and GBrowse)</big>''' ==<br />
===5.1. Is GBrowse being discontinued?===<br />
Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2202_06. All GBrowse tracks and features are now also available in JBrowse. Please use [http://flybase.org/jbrowse/?data=data%2Fjson%2Fdmel&loc=2L%3A2961310..2962310&tracks=Gene_span%2Ctransposable_element_insertion_site&highlight= JBrowse] for your queries.<br />
===5.2. How can I download FASTA sequence from JBrowse? ===<br />
Please find instructions in [https://twitter.com/FlyBaseDotOrg/status/1565058796950396928?s=20&t=Trqw1rNg4EJai5Enk6zoMQ this FlyBase tweetorial].<br />
== '''<big>6. Gene data</big>''' ==<br />
=== 6.1. How can I find transgenic constructs with particular characteristics? ===<br />
Please see the commentary on FlyBase [http://flybase.org/commentaries/2018_08/experimentaltools.html Experimental Tool Reports].<br />
=== 6.2. How can I obtain flanking gene sequence? ===<br />
To obtain flanking sequence for a gene of interest, go to the gene page for that gene. Go to the "Genomic Location" section and click on the "Get Decorated FASTA" link. You can specify the amount of flanking sequence that you wish to have displayed in the "Additional upstream / downstream bases" box.<br />
<br />
You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end for all Dmel genes from the Current Relase page in the Genomes: Annotation and Sequence section.<br />
<br />
The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences.<br />
== '''<big>7. Gene model and genome annotation</big>''' ==<br />
=== 7.1. What happened to my gene? Its gene report says it is withdrawn. ===<br />
Genes are occasionally withdrawn because of a lack of supporting evidence. More commonly, a gene model might be merged with another gene, or split into two or more genes. In such cases, the original gene(s) are withdrawn. You can find the fate and/or history of the withdrawn gene in the Relationship to Other Genes subheading (under Other Information in Gene Reports) in both the withdrawn gene's report and in the report(s) of gene(s) resulting from the merge or split.<br />
=== 7.2. I am trying to compare coordinates between the R6 assembly of the sequenced genome and the dm3 assembly, but the Sequence Coordinate Converter tool does not support Release 3 as an Output Assembly option. ===<br />
The Sequence Coordinate Converter tool does allow this option. The UCSC dm3 reference sequence corresponds to the release_5 (R5) assembly of the ''D. melanogaster'' genome, not the R3 assembly.<br />
===7.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? ===<br />
You have found a gene for which there is a mutation in the sequenced strain. FlyBase has so far identified 64 genes in which a mutation disrupts the coding sequence; we provide a corrected CDS for affected transcripts. Such genes will have a comment about the mutation in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report. You can find the list of affected genes in the [http://flybase.org/docs/releasenotes.tx Release Notes], TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see [http://flybase.org/reports/FBrf0229216.html this FlyBase paper].<br />
===7.4. These two genes map to the same genomic coordinates, and have the same transcript, but FlyBase says they are different genes. How can this be? ===<br />
You have found a pair of dicistronic genes, in which there are two distinct protein coding regions with overlapping transcripts. Dicistronic gene pairs can include both dicistronic transcipts that encode the CDS of both genes, as well as monocistronic transcripts that encode the CDS of only one of the affected genes. Such genes will have a gene_with_dicistronic_mRNA SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about dicistronic genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? ===<br />
You have found a gene with a trans-spliced transcript. Such genes will have a gene_with_trans_spliced_transcript SO entry in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about trans-spliced genes and other exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.6. The protein encoded by this transcript does not include the first ATG in the ORF/extends beyond a stop codon/does not start with an AUG codon. ===<br />
There are a number of exceptional gene model annotations documented in FlyBase. These exceptional cases have strong support from multispecies conservation, protein prediction algorithms, and/or published experimental evidence. Each exceptional case will have a clarifying comment in the 'Comments on Gene Model' subsection of the 'Gene Model and Products' section of the relevant gene report, and/or an informative SO term in the 'Sequence Ontology: Class of Gene' subsection of the of the 'Gene Model and Products' section of the relevant gene report. You can find more information about exceptional annotation cases in the FlyBase paper [http://flybase.org/reports/FBrf0229217.html "Gene Model Annotations for ''Drosophila melanogaster'': The Rule Benders"].<br />
===7.7. What does the annotation release number mean? ===<br />
''D. melanogaster'' annotation numbers combine the BDGP reference genome assembly release number and the FlyBase annotation release number for that reference genome assembly, separated by a decimal. For example, the 2022_05 release of FlyBase included the r6.48 ''D. melanogaster'' annotation set (the 48th annotation set for Release 6 of the reference genome assembly). You can find the annotation number by selecting "Release Notes" from the "About" section of the blue NavBar at the top of every FlyBase page.<br />
NB - the FlyBase annotation number is not associated with the NCBI release number in any way.<br />
===7.8. What reference genome assemblies have been produced for ''D. melanogaster''? ===<br />
''D. melanogaster'' has had 6 reference genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
===7.9. How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates? And where can I find the dm3 genome assembly for ''D. melanogaster''? ===<br />
An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion.<br />
The correspondence of "dm" number to BDGP releases is as follows.<br />
dm1 = Release3<br />
dm2 = Release4<br />
dm3 = Release5<br />
dm6 = Release6<br />
===7.10. How can I submit a correction to the genomic sequence of ''D. melanogaster''? ===<br />
The ''D. melanogaster'' reference genome assembly was generated by the BDGP and represents a specific assembly product using the sequenced strain. It is not within the purview of FlyBase to make corrections to that reference assembly. However, FlyBase can make necessary corrections to gene and transcript annotations - simply [http://flybase.org/contact/email contact us].<br />
===7.11. How can I submit a correction to a gene model of ''D. melanogaster''? ===<br />
If the correction (e.g., new splice isoform, new TSS) is associated with a published paper, please use the Fast-Track Your Paper tool, and under "Genome Annotation Data", tick the box relating to transcript/polypeptide structure changes. Otherwise, please contact us via [http://flybase.org/contact/email the FlyBase contact form] - we can incorporate the data and attribute it to a personal communication.<br />
===7.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for ''D. melanogaster''? ===<br />
NCBI RefSeq transcript annotations for ''D. melanogaster'' are taken directly from the annual FlyBase submission to GenBank. NCBI RefSeq annotations (from FlyBase) are in turn used by the UCSC genome browser. EBI Ensembl ''D. melanogaster'' are obtained directly from FlyBase. As such, FlyBase is the definitive and original source for ''D. melanogaster'' transcript annotations available from most sites.<br />
===7.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? ===<br />
For explanation of FlyBase gene annotation process please see the FlyBase paper [http://flybase.org/reports/FBrf0229216.html "Gene Model Annotations for ''Drosophila melanogaster'': Impact of High-Throughput Data"].<br />
===7.14. What does the annotation release number mean? ===<br />
BDGP genome assemblies are referred to using a 'Release_#' notation. The decimal in FlyBase release notation refers to an annotation set produced by FlyBase that is attached to that assembly; e.g., the release for April 2019 was Release_6.27. Note that feature coordinates will only change with new release assemblies. If you want information on the current assembly and current annotation set, you should look at [http://flybase.org/docs/releasenotes.tx FlyBase's Release Notes], opening up the subsection entitled "''Drosophila melanogaster'' (R#.##)".<br />
<br />
''D. melanogaster'' has had 6 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 and _6 were all BDGP BAC tiling array assemblies taken to a high degree of finishing (except for the uncooperative parts of the centric heterochromatin and a small number of other sizeable regions containing highly repetitive sequences such as the histone gene cluster). Because of the WGS nature of Release_1 and Release_2, producing a coordinate converter for these releases to Releases_3, _4, _5, or _6 is not practically possible.<br />
<br />
The ''D. pseudoobscura'' release 3 assembly was produced by the Baylor HGSC as an improvement to its release 1 and 2 assemblies. The assemblies in FlyBase for the other sequenced Drosophila species are the initial frozen CAF1 assemblies that were produced as part of the same project. More information can be found at the [https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project ''Drosophila pseudoobscura'' Genome Project site].<br />
===7.15. How do I convert coordinates from one genome release to another? ===<br />
You can use the [http://flybase.org/convert/coordinates FlyBase Sequence Coordinates Converter] tool to forward-migrate coordinates from Releases 3, 4 or 5 to Release 4, 5, or 6. There is a link on that page for a tool that offers back conversion from Release 6 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.<br />
===7.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than ''D. melanogaster''? ===<br />
New releases of genomic sequences and gene model annotations of the "other" Drosophila species (other than ''D. melanogaster'') are now managed by NCBI (https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/Drosophila, https://www.ncbi.nlm.nih.gov/genome/annotation_euk/). If you have new or more reliable sequence data, we suggest that you submit your sequence to GenBank. You can then send us a personal communication with the accession number and a description. We will add that communication and the accession number to the gene records affected, so that other users of FlyBase may benefit from your improved data.<br />
<br />
For gene models, if you have sequenced a cDNA, you should submit that sequence to GenBank. We have an automatic pipeline from NCBI for handling cDNA data. The accession number will be incorporated into the gene report and an alignment shown on JBrowse.<br />
<br />
If you do not have a sequenced cDNA, but have a proposed correction determined by other means, you may be able to submit it to GenBank as a TPA (third party annotation). Again, in this case, we would appreciate a personal communication that includes the accession number and a description of the error.<br />
<br />
If your correction cannot be appropriately submitted to GenBank by any of these routes, we will accept it as a personal communication --- but this is not preferrable. The sequence would not be available via BLAST or other queries, nor would it appear as an alignment in JBrowse.<br />
== '''<big>8. Gene name/rename</big>''' ==<br />
===8.1. When (under what circumstances) does FlyBase consider changing a designated gene name? ===<br />
We’re usually quite conservative about making changes, certainly when a symbol/name has been well-used in the literature, so decisions are made on a case by case basis. If it’s clear the relevant community prefers to use a different symbol/name than the current one in FlyBase, we will consider changing it. That decision can be prompted by preferred usage of an alternative in the published literature, or by the interested parties publishing a report or contacting us directly with the intended change. We will also consider a change where a symbol is inaccurate/misleading, is too similar to the symbol of a different gene, is offensive in some way, or to rationalize nomenclature within a gene family, ''etc.''. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here].<br />
== '''<big>9. Job postings</big>''' ==<br />
===9.1. I want to post a job on FlyBase; how can I do that? ===<br />
You can post a position in the FlyBase Forum, which you can reach by clicking the 'Positions Available' icon under the 'Meetings/Courses/Jobs' tab of the External Resources sidebar on the FlyBase homepage.<br />
== '''<big>10. Meetings and courses</big>''' ==<br />
===10.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page?===<br />
Meeting announcements are now hosted at the Fly Research Portal, which you can reach via the 'Meetings Courses' icon in the left sidebar of the FlyBase homepage. Please submit your event using the link at the bottom of the Fly Research Portal Events page.<br />
== '''<big>11. Nomenclature</big>''' ==<br />
===11.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? ===<br />
Yes, there are. Please see our nomenclature guidelines [https://wiki.flybase.org/wiki/FlyBase:Nomenclature#1.2.2 here]. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper.<br />
== '''<big>12. ''Non-melanogaster'' species</big>''' ==<br />
===12.1. I can't find gene model or genome assembly information for my favorite ''non-melanogaster'' Drosophila species. What happened to that information? ===<br />
FlyBase stopped supporting gene model annotation and genome assembly information for species other than ''Drosophila melanogaster'' in Flybase release FB2018_06. You can find the last NCBI annotation update for these species in [http://fb2017_05.flybase.org this FlyBase archived release], and current annotation information at the NCBI page [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/ Eukaryotic genomes annotated at NCBI].<br />
== '''<big>13. Referencing FlyBase</big>''' ==<br />
===13.1. Can I use the FlyBase logo in my publication/poster? ===<br />
The use of the FlyBase logo is permitted unless it is for commercial gain. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
===13.2. I retrieved some information from FlyBase for a publication and wondering how to cite FlyBase in my publication. Are there any guidelines that I can follow? ===<br />
Yes, there are. Please use [https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase this guideline] about citing FlyBase.<br />
== '''<big>14. Stocks</big>''' ==<br />
===14.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? ===<br />
Please contact BDSC [mailto:flystock@indiana.edu directly] at (flystock AT indiana DOT edu).<br />
===14.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? ===<br />
FlyBase does not distribute fly stocks. Please contact the stock center that provides the fly lines you are interested in; FlyBase stock reports include a link to the relevant stock center's order form at the bottom of the report. You can also find a list of stock centers [https://wiki.flybase.org/wiki/FlyBase:Stocks here].<br />
== '''<big>15. Submitting data before publication</big>''' ==<br />
===15.1 I have a preprint. Should I wait for the paper to be published in a peer-reviewed journal, or can I submit some information to FlyBase? ===<br />
If you intend to submit your data for peer-review and publish in a journal, then yes, it would be best to wait for that to happen before adding any information to FlyBase. That way, we know we’re curating the final dataset (following peer-review and any additions/corrections etc) and can attribute the information to the final published account.<br />
===15.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? ===<br />
Yes, we have a way to incorporate unpublished data. Please send us an email with the information so that we can decide whether it is appropriate to add it to FlyBase as a 'personal communication'. You can see the kinds of data appropriate for a personal communication with a QuickSearch References tab query: set the Year field to a range of the last 3 years and Publication type to "personal communication to FlyBase". Additional information about submitting a personal communication can be found [https://wiki.flybase.org/wiki/FlyBase:Personal_communications_to_FlyBase here].<br />
You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org.<br />
== '''<big>16. Web server</big>''' ==<br />
===16.1. How do I access data from an older release that is not available via an active archive server? ===<br />
All data from every release of FlyBase is available via our FTP server (https://ftp.flybase.org/releases ; https://ftp.flybase.org/genomes). Please keep in mind that access to old servers is limited to what you see right now running.<br />
<br />
<br />
{| class="wikitable" style="width: 100%"<br />
! style="text-align: center; width: 50%; background: #C8C8CD" |View [https://wiki.flybase.org/wiki/FlyBase:Help FlyBase Help Index] !! style="text-align: center; width: 750%; background: #C8C8CD" | Do you still have a question? [http://flybase.org/contact/email Contact us].<br />
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