FlyBase:FAQ

FlyBase FAQ

1. Bulk data retrieval 1.1. What sort of bulk data files do you offer? The data sets available are described on the Downloads Overview page. 2. D. melanogaster as a model organism 2.1. Where would I find general information about D. melanogaster? Please check our 'New to Flies' page. 3. Fast-Track Your Paper 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. 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 (FTYP) tool allows you to quickly indicate that your paper has no curatable data types or investigates no Drosophila melanogaster genes. Please tick ’None of the above data types apply’ box in the ‘Data Types’ section when filling the FTYP from. 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"? 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 here. 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. 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. 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'? 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. 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? 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. 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? 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. 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? 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. 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? 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. 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? 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. 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? 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. 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? 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. 4. FlyBase Community Advisory Group 4.1. How can I join the FlyBase Community Advisory Group (FCAG)? Please fill in the FCAG registration form. 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? Please fill in the FCAG registration form, so that we can update your information in our database. 5. FlyBase fee 5.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? You can pay the FlyBase fee at this link. We also have a dedicated FlyBase Fees FAQ. Please contact us to discuss institutional/departmental/corporate fees. 6. FlyBase people database 6.1. Is FlyBase people database still active? No, the FlyBase people database was retired. 7. Genome browser (JBrowse and GBrowse) 7.1. Is GBrowse being discontinued? Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2022_06. All GBrowse tracks and features are now also available in JBrowse. Please use JBrowse for your queries. 7.2. How can I download FASTA sequence from JBrowse? Please find instructions in 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). 8. Gene data 8.1. How can I find transgenic constructs with particular characteristics? Please see the commentary on FlyBase Experimental Tool Reports. 8.2. How can I obtain flanking gene sequence? 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. 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. The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences. 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? You are welcome to send us a proposed update. You may do so by using our contact form and by selecting “Gene Snapshots” as the subject of your message. 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? 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. 9. Gene model and genome annotation 9.1. What happened to my gene? Its gene report says it is withdrawn. 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. 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. 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. 9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? 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 Release Notes, TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see this FlyBase paper. 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? 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 "Gene Model Annotations for Drosophila melanogaster: The Rule Benders". 9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? 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 "Gene Model Annotations for Drosophila melanogaster: The Rule Benders". 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. 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 "Gene Model Annotations for Drosophila melanogaster: The Rule Benders". 9.7. What does the annotation release number mean? 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. NB - the FlyBase annotation number is not associated with the NCBI release number in any way. 9.8. What reference genome assemblies have been produced for D. melanogaster? 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. 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? An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion. The correspondence of "dm" number to BDGP releases is as follows. dm1 = Release3 dm2 = Release4 dm3 = Release5 dm6 = Release6 9.10. How can I submit a correction to the genomic sequence of D. melanogaster? 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 contact us. 9.11. How can I submit a correction to a gene model of D. melanogaster? 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 the FlyBase contact form - we can incorporate the data and attribute it to a personal communication. 9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for D. melanogaster? 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. 9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? For explanation of FlyBase gene annotation process please see the FlyBase paper "Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data". 9.14. What does the annotation release number mean? 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 FlyBase's Release Notes, opening up the subsection entitled "Drosophila melanogaster (R#.##)". 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. 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 Drosophila pseudoobscura Genome Project site. 9.15. How do I convert coordinates from one genome release to another? You can use the 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. 9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than D. melanogaster? 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. 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. 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. 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. 9.17. Where can I find FlyBase data for older genome assemblies? FlyBase archives the annotation files (FASTA, GFF, GTF) generated for every release on our 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)". The full list of past FlyBase releases is available on our 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". 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. 10. Gene name/rename 10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? 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 here. 11. Job postings 11.1. I want to post a job on FlyBase; how can I do that? 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. 12. Meetings or courses 12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page? 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. 13. Nomenclature 13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? Yes, there are. Please see our nomenclature guidelines here. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper. 14. Non-melanogaster species 14.1. I can't find gene model or genome assembly information for my favorite non-melanogaster Drosophila species. What happened to that information? 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 this FlyBase archived release, and current annotation information at the NCBI page Eukaryotic genomes annotated at NCBI. 15. Single-cell RNA-sequencing data 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? The only thing you have to do is to make your raw data files available in a public data store, such as the NCBI’s Gene Expression Omnibus or the 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. 16. Referencing FlyBase 16.1. Can I use the FlyBase logo in my publication/poster? The use of the FlyBase logo is permitted unless it is for commercial gain. Please use this guideline about citing FlyBase. 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? Yes, there are. Please use this guideline about citing FlyBase. 17. Stocks 17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? Please contact BDSC directly at (flystock AT indiana DOT edu). 17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? 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 here. 17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? Please send us a personal communication using 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. 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. 18. Submitting data before publication 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? 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. 18.2. I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? 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 here. You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org. 19. Data from older releases 19.1. How do I access data from an older release? 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 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 FTP files, so they can figure out how to recapitulate searches done on the full website. 20. How to ...? 20.1. How to download the bulk data table (specifying FlyBaseID, Associated Gene, Allele Class and Phenotypic Class) of all recessive alleles that give a lethal phenotype? Quick Search on FlyBase Home Page > Phenotype > Phenotypic class: lethal (use 'increased mortality during development' term if you are interested in partially lethal alleles/genes as well) > refinement: recessive > Search > Export > ID list (download) FlyBase Home Page > Batch Download > Paste the downloaded ID's > Data Source: Report fields > Send results to: File > Next > Check 'Associated gene', 'Allele class' and 'Phenotypic Class' > Get Field Data 1. Bulk data retrieval 1.1. What sort of bulk data files do you offer? The data sets available are described on the Downloads Overview page. 2. D. melanogaster as a model organism 2.1. Where would I find general information about D. melanogaster? Please check our 'New to Flies' page. 3. Fast-Track Your Paper 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. 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 (FTYP) tool allows you to quickly indicate that your paper has no curatable data types or investigates no Drosophila melanogaster genes. Please tick ’None of the above data types apply’ box in the ‘Data Types’ section when filling the FTYP from. 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"? 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 here. 3.3. I just went to Fast-Track a recent publication but it was not found by the FlyBase "Fast-Track Your Paper" tool. 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. 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'? 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. 3.5. I submitted an FTYP form but my data is not visible on FlyBase. When will it show on the relevant gene reports? 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. 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? 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. 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? 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. 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? 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. 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? 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. 3.10. We completed the FTYP form but we did not receive any feedback/message confirmation. Should we complete it one more time? 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. 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? 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. 4. FlyBase Community Advisory Group 4.1. How can I pay the FlyBase fee? Can I pay the fee for my entire lab/institution/company? Please fill in the FCAG registration form. 4.2. I am a current member of the FCAG. I have moved to a new institution, so could you please update my details? Please fill in the FCAG registration form, so that we can update your information in our database. 5. FlyBase fee 5.1. How can I join the FlyBase Community Advisory Group (FCAG)? You can pay the FlyBase fee at this link. We also have a dedicated FlyBase Fees FAQ. Please contact us to discuss institutional/departmental/corporate fees. 6. FlyBase people database 6.1. Is FlyBase people database still active? No, the FlyBase people database was retired. 7. Genome browser (JBrowse and GBrowse) 7.1. Is GBrowse being discontinued? Yes, GBrowse is no longer being maintained, and GBrowse access will be discontinued in FlyBase release FB2022_06. All GBrowse tracks and features are now also available in JBrowse. Please use JBrowse for your queries. You can watch Using JBrowse on FlyBase video tutorial for further information. 7.2. How can I download FASTA sequence from JBrowse? Please find instructions in 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). 8. Gene data 8.1. How can I find transgenic constructs with particular characteristics? Please see the commentary on FlyBase Experimental Tool Reports. 8.2 How can I obtain flanking gene sequence? 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. 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. The file: dmel-all-gene_extended2000-r6.nn.fasta contains these sequences. There is also a file with all intergenic sequences. 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? You are welcome to send us a proposed update. You may do so by using our contact form and by selecting “Gene Snapshots” as the subject of your message. 8.4. How do I find a cDNA that corresponds to a specific transcript of a gene with alternative splice isoforms? 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. 9. Gene model and genome annotation 9.1. What happened to my gene? Its gene report says it is withdrawn. 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. 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. 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. 9.3. I translated a transcript for a protein, and that protein is different from the one FlyBase displays. Why is there this inconsistency? 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 Release Notes, TABLE 5: Genes with Known Disruptive Mutations in the iso-1 Reference Sequence. Please also see this FlyBase paper. 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? 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 "Gene Model Annotations for Drosophila melanogaster: The Rule Benders". 9.5. Part of this transcript is on the positive strand, and part is on the negative strand. Is there a mistake? 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 "Gene Model Annotations for Drosophila melanogaster: The Rule Benders". 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. 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 "Gene Model Annotations for Drosophila melanogaster: The Rule Benders". 9.7. What does the annotation release number mean? 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. NB - the FlyBase annotation number is not associated with the NCBI release number in any way. 9.8. What reference genome assemblies have been produced for D. melanogaster? 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. 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? An alternative "dm" numbering system from UCSC has sometimes been used to refer to the BDGP reference genome assemby releases, often causing confusion. The correspondence of "dm" number to BDGP releases is as follows. dm1 = Release3 dm2 = Release4 dm3 = Release5 dm6 = Release6 9.10. How can I submit a correction to the genomic sequence of D. melanogaster? 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 contact us. 9.11. How can I submit a correction to a gene model of D. melanogaster? 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 the FlyBase contact form - we can incorporate the data and attribute it to a personal communication. 9.12. How do FlyBase transcript annotations compare to NCBI RefSeq annotations for D. melanogaster? 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. 9.13. Why are all theoretically possible transcripts of a gene not annotated ? How does FlyBase decide which transcripts to annotate? For explanation of FlyBase gene annotation process please see the FlyBase paper "Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data". 9.14. What does the annotation release number mean? 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 FlyBase's Release Notes, opening up the subsection entitled "Drosophila melanogaster (R#.##)". 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. 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 Drosophila pseudoobscura Genome Project site. 9.15. How do I convert coordinates from one genome release to another? You can use the 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. 9.16. How can I submit a correction to the genomic sequence or gene model of a Drosophila species other than D. melanogaster? 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. 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. 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. 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. 9.17. Where can I find FlyBase data for older genome assemblies? FlyBase archives the annotation files generated for every release on our 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)". The full list of past FlyBase releases is available on our 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". 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. 10. Gene name/rename 10.1. When (under what circumstances) does FlyBase consider changing a designated gene name? 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 here. 11. Job postings 11.1. I want to post a job on FlyBase; how can I do that? 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. 12. Meetings and courses 12.1. I am organizing a Drosophila meeting. How can I add this meeting to the Drosophila Meetings page? 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. 13. Nomenclature 13.1. I identified a gene and would like to name it. Are there any FlyBase guidelines for this? Yes, there are. Please see our nomenclature guidelines here. We recommend mentioning a unique FlyBase identifier (FBgn#) along with the new name in your paper. 14. Non-melanogaster species 14.1. I can't find gene model or genome assembly information for my favorite non-melanogaster Drosophila species. What happened to that information? FlyBase stopped supporting gene model annotation and genome assembly information for species other than Drosophila melanogaster in Flybase release FB2018_06. NCBI has taken over the maintenance of non-melanogaster Drosophila annotations, which can be found here: Eukaryotic genomes annotated at NCBI. There are 40 Drosophila genomes listed under "Insects". For each annotated genome listed, there are options for file download (FTP), BLAST (B), Annotation Report (AR) and genome data viewer (GDV). In the GDV, there is a "Search assembly" box that does seem to recognize at least some D. melanogaster gene names and navigates to that species' ortholog: e.g., wg, dpp, though not CG46525 or CG46525. Another entry point into the NCBI genome browser is to use the "BLAST genome" option under the "More Tools" option in the top menu. So, for example, you can get the sequence of a D. melanogaster gene using the FlyBase Sequence Downloader tool, then BLAST against the non-melanogaster genome of your choice. This generates an "RID" for that BLAST search, which then becomes visible in the "BLAST" drop down menu to the left of your genome browser. 15. Single-cell RNA-sequencing data 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? The only thing you have to do is to make your raw data files available in a public data store, such as the NCBI’s Gene Expression Omnibus or the 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. 16. Referencing FlyBase 16.1. Can I use the FlyBase logo in my publication/poster? The use of the FlyBase logo is permitted unless it is for commercial gain. Please use this guideline about citing FlyBase. 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? Yes, there are. Please use this guideline about citing FlyBase. 17. Stocks 17.1. I would like to donate some flies to Bloomington Drosophila Stock Center. What is the procedure for this? Please contact BDSC directly at (flystock AT indiana DOT edu). 17.2. How can I obtain a stock listed in FlyBase? Can I order that stock from FlyBase? 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 here. 17.3. I got a stock from FlyBase and I found something about that stock that the community should know. What can I do? Please send us a personal communication using 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. 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. 18. Submitting data before publication 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? 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. 18.2 I have some experimental data that I am not planning on publishing. Can I submit those data to FlyBase? 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 here. You might also consider if your data is appropriate for a micropublication in https://www.micropublication.org. 19. Data from older releases 19.1. How do I access data from an older release? 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 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 FTP files, so they can figure out how to recapitulate searches done on the full website. 20. How to ...? 20.1. How to download the bulk data table (specifying FlyBaseID, Associated Gene, Allele Class and Phenotypic Class) of all recessive alleles that give a lethal phenotype? Quick Search on FlyBase Home Page > Phenotype > Phenotypic class: lethal (use 'increased mortality during development' term if you are interested in partially lethal alleles/genes as well) > refinement: recessive > Search > Export > ID list (download) FlyBase Home Page > Batch Download > Paste the downloaded ID's > Data Source: Report fields > Send results to: File > Next > Check 'Associated gene', 'Allele class' and 'Phenotypic Class' > Get Field Data View FlyBase Help Index Do you still have a question? Contact us.