We would like to announce the availability of the WormBase WS261 release on the WormBase website and FTP.
WormBase now provides the canonical gene set for each species in Gene Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html). These files can be used directly by a number of popular sequence analyses tools (e.g. Cufflinks).
The GTF files are available from the WormBase FTP site, for example, the GTF file for C. elegans, c_elegans.PRJNA13758.WS253.canonical_geneset.gtf.gz, is available here.
In the previous WS246 release we introduced automated gene descriptions for C. elegans genes that lacked a manually written one. These gene descriptions include information related to orthology, process, function and sub-cellular localization (when these data-types have been curated in the WormBase database), giving the user a quick overview of the gene. The current WS247 release includes automated descriptions for over 18,000 C. briggsae genes. Check out the C. briggase gene pages to view these descriptions under ‘Overview’! In future releases, we will add genes from many more species! Also, WormBase is working on user-friendly forms which you can use to edit these descriptions and make them better.
* Data from Inparanoid was updated to version 8
* Orthology data for all core nemtatodes and model organisms was imported from WormBase Parasite release 1
* OMA and TreeFam data was removed in preparation for an update (TreeFam accessions will remain as database crossreferences)
Expression and Picture update
* A large set of expression graphs for other nematodes produced by Yanai’s has been added
The RNASeq data will become richer in WS247.
There will also be “control” mean and median FPKM values derived from the data which does not have a specific experimental condition applied.
New/updated reference genomes
This release we see a rebuild of C. elegans, B. malayi and O. volvulus. Various data classes and curational activites have been undertaken on these species since the release of WS246