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.
Alliance of Genome Resources new version released
Worm folks-check out the latest release of the Alliance of Genome Resources (Version 5.2.1) to access harmonized data across all the major model organisms. Lately, the Alliance has had an orthology data refresh and is using the latest version of the DRSC Integrative Ortholog Prediction Tool (DIOPT): Version 9. This version includes a data refresh from all orthology sources, the addition of the SonicParanoid algorithm, and the removal of both TreeFam and RoundUp data sources. For complete updates be sure to look at the Alliance News and Release Notes.
For miRNA fans
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!
New operons in C. briggsae
Kindly, Dr. Itai Antoine Toker made us aware of the paper Uyar et al. Genome Research 2012 (PMID: 22772596/ WBPaper00041271), which contains a genome-wide set of operon predictions for C. briggsae. The data was mapped forward to the current gene set using the Sequence IDs supplied. 1034 operons were captured from the publication, but because of the time between publication and extensive re-annotation of C. briggsae only 709 of these operons had enough information to allow us to map them precisely onto the genome and supplement the C. briggsae operon JBrowse track. If you find some interesting dataset you’d like WormBase to curate, please let us know at help@wormbase.org