New Organization of D melanogaster GBrowse Views
Beginning with the last FlyBase release for 2011 (FB2011_10), you will see a new and more biologically meaningful organization of the genomic data presented on GBrowse for D. melanogaster. The explosion of genetic and functional genomic data sets for D. melanogaster necessitated the subdivision of these data into different ‘data source views’ to efficiently utilize the space and optimize performance, but the original subdivisions grew organically instead of according to optimal biological meaning. This has been corrected. There are currently four views for D. melanogaster (see figure below):
- Gene Models/Evidence contains all the evidence related to the structure of our gene models. This includes such tracks as gene predictions, aligned cDNAs, and orthology information.
- Expression/Regulation contains all the information relevant to how genes are expressed and regulated. This includes tracks such as RNA-Seq by developmental stages, transcription factor binding sites, and enhancers.
- MegaView contains tracks which require a very ‘zoomed out’ view. With MegaView, entire chromosome arms can be viewed at once, allowing large features such as aberrations and duplications to be viewed in their entirety.
- Gene Disruptions, Stocks, and Reagents contains information relevant to mutations which have been localized to the sequence, reagents such as RNAi amplicons, and stock center data. Stock center data includes both the Bloomington Deficiency Kit lines as well as transgene insertions available from the various stock centers.
When using GBrowse, it is possible to toggle between the various views simply by selecting a different option from the Data Source menu. The genomic region that is being viewed will remain the same.
Help documentation is available for every track grouping. Click on the link just above the Tracks selection area of each GBrowse view page. Each track name is also a link to the help document for the view; these links will scroll the help page directly to the documentation about that track.
We invite your feedback on this reorganization. In particular, if there are certain tracks that are currently only available on different views that you’d like to be able to see in a single view, please let us know using the 'Contact FlyBase' form.