New Alliance release available

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Check out the new Alliance release 7.0.0. To learn more about this release please see the release notes.

If you don’t already know about the Alliance of Genome Resources (Alliance), it is a consortium of 7 model organism databases (MODs) and the Gene Ontology (GO) Consortium whose goal is to provide an integrated view of their data to all biologists, clinicians and other interested parties. You can look at harmonized C. elegans data such as disease model annotations in the context of other species. You can find ortholog data easily right on a gene page. Note that we are in the process of transitioning data types from WormBase to the Alliance and building data displays for these data, so not all WormBase data is available at the Alliance yet.

For miRNA fans

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For miRNA fanatics out there, we have added 90 miRNA gene clusters from MirGeneDB to the C. elegans annotation in release WS284. This complements the 20 clusters (800 objects) which were already there, making the WormBase miRNA collection possibly the most complete in the world. You can access the miRNAs through the web pages https://wormbase.org/search/all/miRNA, or through JBrowse tracks “Curated Genes(noncoding)” e. g. And don’t forget WormBase also has an impressive collection of other non-coding RNAs as well; circRNAs, lincRNAs, piRNAs, snRNA, snoRNAs, precursors and many more. Happy investigating!

WormBase release WS282

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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.

New version of the Alliance of Genome Resources

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A new release (4.1.0) of the Alliance of Genome Resources (Alliance) is now available. Search for your favorite gene and find harmonized data such as gene function, disease models, phenotypes, expression and many more across orthologous model organisms and human. Read about the new data and features in the release notes.

WormBase updates in WS277 – new protein schematic images!

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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.