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.

Change to disease statements in gene descriptions for WS279

Due to non-stringent human ortholog(s) and their associated diseases, C. elegans gene descriptions (displayed in the “Overview widget” of gene pages) often had spurious diseases associated with their human orthologs. With WS279, we imposed a stringency filter and only those disease associations to ortholog(s) called by more than one orthology prediction method are included in the gene description. This change has improved the accuracy of statements that read “human orthologs of this gene are implicated in <disease(s)>”. However, please note that this change has also resulted in the loss of such statements for several hundred gene descriptions due to the increased stringency.

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: We’ve updated the protein schematic image in the homology widget on protein pages (see, for example, the UNC-2, isoform a 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 — the genome browser at WormBase — 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.  The previous static protein schematic image remains available by clicking on the “Legacy Protein Schematics” 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.