Enrichment, ontology browser and graph display tools are all working again. Thank-you for your patience.
A disk failure on one of our servers has brought the gene set enrichment analysis tool (TEA), the Ontology Browser (WoBr) and the graph display tool on the gene page down. We are working to restore these tools as soon as possible and apologize for any inconvenience caused. We will let the community know as soon as these are restored.
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.
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.