WS273 version of WormBase

Please note that the WS273 version of WormBase is live on our website.  The release notes for this version contain a detailed report of the various entities (eg. gene, allele) and the number of sequence and biological annotations.

Some of the highlights are:

C.elegans Nanopore data has been integrated and is being used to improve UTR annotation. Further work on improving our automatic transcript annotation is ongoing.

This release includes a few hundred gene splits in Pristionchus pacificus predicted by the Sommer lab based on IsoSeq analysis. More will be included in future releases.

WormBase updated to the WS270 release

Alliance orthologs

Starting from WS270 we are using the Alliance of Genome Resources for orthologs between model organism genes. This should be more comprehensive and include the latest data from our sister databases.

VC2010 genome

An assembly and geneset of the VC2010 C.elegans strain has been added and work is ongoing to improve the integration and display of strain specific data. Additionally more mappings of N2 annotation will be included in future releases.

WS267 release of WormBase

Please note that the WS267 release of WormBase is now live.  The complete release notes for WS267 can be viewed here.  Some of the highlights include–

Trichuris muris update
Trinity assembled RNASeq reads from publicly available short read data at SRA have been added to Trichuris muris as additional track and alignments. In addition IsoSeq data from long-range PacBio data (provided by the Berriman lab), corrected by genome alignment has been used as additional source to build transcript models.

In addition the Trichuris muris ncRNA gene set has increased from 26 to 759 following the integration of data produced by the WormBase Parasite ncRNA prediction pipeline. These transcripts have been fully integrated with stable IDs and associated naming and meta data.

Gene descriptions for T. muris will be coming in the WS268 release of WormBase.

Brugia malayi update
New gene models provided by the Beech lab for Parasitology at the McGill University have been merged into the official gene set.

WS266 release

Please note that the WS266 version of WormBase has been released! The release notes for this release describe the data types and their numbers. A list of all files available on our FTP site can also be viewed.  Changes in this release include the following:

Physical Interaction data curation

We have added over 5000 manually curated physical interactions which include binary protein-protein interactions as well as protein interactions that occur in a protein complex. Protein-protein interaction data can be found as a part of physical interaction data in the Interactions widget on the gene page. The Interactions widget provides different types of interaction data related to the gene of interest, such as physical, genetic, regulatory, and predicted interactions.

 

Protein Identifiers

We have made a change to our internal identifiers for nematode protein sequences. Previously, we prefixed each identifier with *two* prefixes to denote which  species the protein is from, e.g. WP:CE00001. We have removed the first prefix (the “WP:”) from these identifiers.

Since these prefixes are almost entirely invisible on the site and have never been used by external resources hosting worm data (e.g. UniProt), this change should not affect most users.