WormBase is updated to WS260

The 260th version of WormBase has been released!  The release notes that are published with each new release gives you various statistics about the data in the current release as well as providing a quick peak at the breath and depth of the data in WormBase.  It also lists all the data files available for download at our FTP site.  Check all of these out and let us know if you have any suggestions or questions!

Gene Transfer Format (GTF) files now available

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.

 

WS247: C. briggsae genes have descriptions!

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.

Ascaris suum genome in WormBase

The newly published Ascaris suum genome (Aaron Jex, et al, Nature 2011 Oct 2) is available at WormBase including it’s geneset. The data has been added to GBrowse/BLAT/BLAST and can be downloaded as FASTA/GFF3 files from the WormBase FTP server.

Ascaris suum is a model for other parasitic Ascaris, as well as causing itself economic damage to pig farming. In addition it is known to be resistant to a large number of antihelminth chemicals.