Difference between revisions of "FlyBase:FAQ"
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Revision as of 16:53, 19 February 2014
- 1 How can I obtain a stock listed in FlyBase?
- 2 What is Arm U in Drosophila melanogaster?
- 3 How can I submit a correction to the genomic sequences of a Drosophila species other than D. melanogaster?
- 4 Where can I find information on Drosophila Gold Collection clones?
- 5 Do you provide decorated FASTA sequences for gene ... ?
- 6 How can I obtain flanking gene sequence?
- 7 How can I obtain an Exelixis Clone?
- 8 What sort of bulk data files do you offer?
- 9 How do I cite the Drosophila phylogeny?
- 10 How can I search the abstracts of the Annual Drosophila Research Conference?
- 11 What does the annotation release number mean?
- 12 How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates?
- 13 How do I print FlyBase pages accurately?
How can I obtain a stock listed in FlyBase?
Questions about individual stocks listed in FlyBase should be directed to the collection that holds the stock. For collections with web sites, the name in the "Collection" field of the FlyBase Stock Report links to the collection's web site, where contact information can be found. For laboratory collections that do not have web sites, an e-mail address is included in the "To Request Stock" field of the FlyBase Stock Report.
What is Arm U in Drosophila melanogaster?
Arm U is an unordered assembly of unplaced sequence scaffolds. More information about Arm U can be found in the GenBank record (FA000001).
Here is the comment section from this record:
This record is an unordered assembly of unplaced (chrUn) sequence scaffolds that lie in heterochromatic regions of the genome, and does not reflect the structure of a biological molecule. Intervals between scaffolds are denoted by 100 N's, and the order and orientation of the scaffolds with respect to one another is not known. Scaffolds joined in this record either cannot be localized to a particular chromosome or have conflicting localization data. It is provided for the FlyBase Consortium as an aid for sequence tracking. For further information about this sequence, please visit our Web site (http://www.dhgp.org). WARNING: The order and orientation of scaffolds in this record are unknown.
How can I submit a correction to the genomic sequences of a Drosophila species other than D. melanogaster?
At the present time, the genomic sequences of the "other" Drosophila species (other than D. melanogaster) are static; there are no immediate plans to incorporate corrections. Since FlyBase does not store original 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 of the error. 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 GBrowse.
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 GBrowse.
Where can I find information on Drosophila Gold Collection clones?
If there is a full length DGC clone associated with a gene you will find it in the gene report under the REAGENTS/cDNA section in its own field. For example: Dmel\lark lists LD40792 as a DGC clone.
If the "DGC cDNAs" field does not appear in a report it means that a DGC clone has not been identified for the gene.
Do you provide decorated FASTA sequences for gene ... ?
This works for some genes but not others. A work around for this until we get it fixed is to use the GBrowse 'Download sequence ' option. Here's how it works:
Using Dlic2 (CG1938) as an example, copy the coordinates from the 'Physical map' field of the annotation report into the GBrowse 'Find Genome Region' window. This displays X:10999619..11008430 in GBrowse. In the 'Feature Tracks' panel select the features you're interested in and update the map. Then open the 'Download sequences' panel toward the bottom of the page. From the 'Dumps,...' menu select 'Dump Decorated FASTA file' and choose 'Configure'. Select display settings to distinguish the features you're interested in.
How can I obtain flanking gene sequence?
Unfortunately there is not an easy way to get the flanking sequences for a specific subset of genes in FlyBase. You can get a multiple FASTA file containing the gene region sequences including 2000 bp flanking on either end from the ftp site.
The file: dmel-all-gene_extended2000-r4.2.1.fasta contains these sequences. There is also a file with all intergenic sequences.
You would then need to identify your genes of interest and pull out the section of sequence you were interested in.
How can I obtain an Exelixis Clone?
Unfortunately Exelixis made the decision not to save their libraries as they felt the clones were largely overlapping with existing ones. Obviously that is not truly the case but that is the situation so none of these clones are available.
What sort of bulk data files do you offer?
How do I cite the Drosophila phylogeny?
The Drosophila phylogeny shown on FlyBase is a compilation of information that can be found in:
A Powell, J.R. 1997 Progress and Prospects in Evolutionary Biology: The Drosophila Model.
BIOSIS ID: 1102964
Oxford University Press, Inc.
How can I search the abstracts of the Annual Drosophila Research Conference?
From this, you can go to the abstract search page to find your abstract-of-interest, for example:
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 February 2010 was Release_5.25. 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 5 genome assemblies produced by BDGP. Release_1 and Release_2 were Celera whole genome shotgun (WGS) assemblies, whereas Releases_3, _4, _5 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 is not practically possible.
The D. pseudoobscura release 2 assembly was produced by the Baylor HGSC as an improvement to its initial release 1 assembly. 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 AAA site.
How do FlyBase/GenBank/BDGP assembly coordinates relate to UCSC coordinates?
The UCSC assembly numbers dm1 through dm3 correspond to BDGP/FlyBaseGenBank assemblies Release 3 through Release 5.
You can use the FlyBase Coordinate Converter tool to forward-migrate coordinates from Release 3 to Release 4, or from Release 4 to Release 5. No tool exists for migrating from BDGP/FlyBaseGenBank Releases 1 or 2.
How do I print FlyBase pages accurately?
We realize that many people like to print out the information provided by FlyBase, however some of the current browsers do not render the new FlyBase pages particularly well. If you routinely print out a significant amount of information from FlyBase we recommend that you use Opera as your browser. While many other browsers will print the information included in a report, at this time only Opera will print the page format properly (including colors and shading).
If your work requires that you print the page exactly as it appears on your monitor and you do not wish to install Opera, we suggest that you print a screen shot of the page. Instructions on how to take a screen shot on different platforms are given below.
- Open the application "Microsoft Word"
- Click on the web browser and arrange the information you would like to print within the window
- Press the key combination "Alt-PrintScreen"
- Click on the "Microsoft Word" window to activate it and press the key combination "Ctrl-V" to paste the image into the window
- Press the key combination "Ctrl-P" to enter the print dialog of the application. Under the Zoom section of the dialog box set the "Scale to paper size" option to the size of the paper used in your printer, then press "OK".
- Open the application "Grab" in the "Utilities" folder.
- From the Capture menu select "Window" (or press the key combination "Shift-Command-W")
- Select "Choose Window", and click on the browser window you wish to capture.
- A image of the browser will appear in a new window.
- To print the image click on "Page Setup.." under the File menu and set "Scale" as 50%, press "OK", and then enter the print dialog by pressing the key combination "Command-P"
- Open the application "Preview"
- Press the key combination "Control-Command-Shift-4", then press the space bar.
- Move the pointer over the browser window so that it is highlighted, then click.
(NB: You can cancel the operation by pressing the escape key)
- Activate Preview by clicking on its icon
- Press the key combination "Command-N" to create an image of the web browser.
- Press the key combination "Command-P" to enter the print dialog
(In this case the page is scaled to fit the page by default)
If you use Safari consider installing the free program Netfixer that allows you to capture an image of an entire webpage no matter its "length".