WormBase updated to WS276

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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.

WormBase version WS274 released

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Please note that WormBase version WS274 was released and is the current release now live on the website. The version of the C. elegans reference genome in this release is WBcel235, included since WS235.

Highlights of this release include:

  1. Isoseq data which was presented at the PacBioNorth America User Group meeting. We applied the PacBio post processing pipeline as described here. The resulting sequences are including in the transcript alignments and will be visible on the genome browser. They will also be included in our automatic transcript generation pipeline in a future release of WormBase.
  2. Improved code to generate non-redundant transcripts. Each CDS should now have only unique transcripts.
  3. Improved interaction data display in the Interactions widget: New Venn diagram for the different types of interactions-physical, genetic and regulatory.

For a complete and more detailed list of changes for this release please see:

https://wormbase.org//about/wormbase_release_WS274#0–10













WS273 version of WormBase
 

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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
 

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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
 

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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.