Check out the new release (version 7.4.0) of the Alliance of Genome Resources (Alliance). A notable feature of this release is that it includes ~2.5 million variants of clinical significance from ClinVar! To learn more about this release see the Release Notes.
WormBase Parasite launches new release
WormBase ParaSite launches its new release 17 with an exciting list of new/updated genomes and new features:
- Integration of AlphaFold 3D protein structures for 8 species.
- Addition of 11 new genome assemblies of which 6 are new species.
- Annotation updates for 2 genomes.
- Gene-phenotype associations are now available in our FTP directory.
- Improvements in the way external gene synonyms are integrated and displayed.
- Deployment of WebApollo instances for more species to further facilitate community curation.
For more information please see the WormBase ParaSite blog.
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.
New release of WormBase: WS279
WormBase has been updated to the WS279 release of the database. In this release, we’ve refined the feedback mechanism and improved error handling behind the scenes. You can read more about the curation statistics of the WS279 release in the release notes.
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.