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.

Alliance of Genome Resources 3.1 released

The Alliance of Genome Resources is a portal for data related to six of the major model organisms and human data. The Alliance has been updated to the 3.1 release and contains new features and new data. Key new features include a refined home page and an allele page that includes transgenic alleles and shows variant consequences for transcripts. The Alliance also provides a Java API for access to the data. For a complete list of 3.1 features please see the release notes.

WormBase updated to WS276

A new release of WormBase, WS276 is live on the website. Please see the release notes which contain complete information about this release.

Data changes: note that C. elegans gene descriptions in the “Overview” section of gene pages have improved orthology statements to human genes. WormBase uses the DIOPT orthology data from the Alliance of Genome Resources and has increased stringency by displaying only those human orthologs that have been determined by three or more methods. This should significantly improve the orthology data in WormBase which is also reflected in the gene descriptions. 

Known Issues: the circRNAs failed mapping so sequence and genomic position are not available for this release, but will be in the WS277 release.

microPublication Biology is now indexed in PubMed

WormBase is happy to announce that the microPublication Biology journal is now fully listed in PubMed!

To make articles easier to cite and discover, every microPublication now receives a PubMed ID, a PubMed Central ID, and a DOI. If you have published with us in the past, consider updating your citations. Indexing is retroactive for all past articles.

You can see microPublications in PubMed by browsing the full index at
PubMed Central. Or look for microPublications during normal searches at PubMed or PubMed Central.

We look forward to receiving more submissions!

Check out Venn diagrams for interaction data in WormBase

WormBase curates four different types of gene-to-gene interaction data: genetic, regulatory, physical, and predicted. These data are found in the interactions widget in each gene page. Aside from the predicted interactions, the other three types are curated with direct experimental evidence from the literature. Check out the micropublication which describes the Vennter tool. This tool is integrated into the interactions widget on WormBase gene pages and allows the visualization and analyses of interaction data.