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
3D structures for all proteins
AlphaFold is an AI system, created in partnership between DeepMind and the EMBL-European Bioinformatics Institute (EMBL-EBI), that makes predictions of a protein’s structure from its amino-acid sequence. Go to their webpage to look at your favourite protein from C. elegans, Brugia, Onchocerca, Strongyloides, Trichuris or Wuchereria. If your favourite protein is missing, remember that any protein with >90% amino acid similarity is quite likely to have a very similar structure. And if you spot any structure that does not look right contact help@wormbase.org, and we’ll forward your feedback.
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 single-cell RNA seq data from CeNGEN
Single-cell RNA-Seq data from the CeNGEN consortium
http://www.cengen.org/ are now available on WormBase! Check out the ‘Expression’ widget for your favorite gene page to explore the CeNGEN gene expression graphs. WormBase will integrate more CeNGEN data in future releases.
New release of WormBase ParaSite
Release 16 of WormBase Parasite has gone live. Read about it here: https://wbparasite.wordpress.com/2021/09/06/announcing-wormbase-parasite-release-16/