As you know WormBase is harmonizing, transitioning and displaying data at the Alliance of Genome Resources (Alliance). Check out the latest version of the Alliance (7.5.0) for data related to your favorite model organism and other ones! Don’t forget to look at the release notes which explain the details of this release. Please note that all WormBase data is not yet available at the Alliance, we thank you for your patience and understanding during the transition period.
WormBase release WS282
New release of Wormbase WS282 is out. Details related to the data and changes in WS282 are available in the release notes.
A highlight of this release is that variant data are now also available in VCF file format:
c_elegans.PRJNA13758.WS282.variations.vcf.gz and c_briggsae.PRJNA10731.WS282.variations.vcf.gz
These files are available in the respective “species” folder on the WormBase FTP site.
WormBase updates in WS277 – new protein schematic images!
We have released the 277th version of WormBase! As always, for a detailed report please look at the WS277 release notes.
New features: Weāve updated the protein schematic image in the homology widget on protein pages (see, for example, theĀ UNC-2, isoform aĀ page.) This image displays protein domains and exons mapped to amino acid coordinates, making it easy to see which regions of a transcript correspond to specific features. Driven by JBrowse ā the genome browser at WormBase ā users can click through the image to an interactive view in amino acid coordinates. From that familiar interface, one can scroll, export sequence (can they?), get additional information on specific features, and zoom in to single amino acid residue resolution, color-coded by chemical property.Ā The previous static protein schematic image remains available by clicking on the āLegacy Protein Schematicsā link, but will be removed after the WS278 release.
New data sets:
C. elegans: Additional Nanopore transcript data has been added.
C. elegans VC20210: The VC2010 strain data includes gene annotation which has been manually curated to improve the coding gene structures lifted over from the N2 strain annotation. This process is substantially complete, with some work still to be done on chromosome X. The number of coding genes which do not map correctly has been reduced so far from around 400 down to 50 genes which cannot yet be located and 10 which appear to be pseudogenes in VC2010. There are 20 genes which appear to be duplicated in N2 and have disappeared in VC2010. There have been 39 novel coding genes created.
WormBase is updated to WS260
The 260th version of WormBase has been released! Ā 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. Ā It also lists all the data files available for download at our FTP site. Ā 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.