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.

Alliance of Genome Resources updated

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The Alliance (alliancegenome.org) 3.0 version released yesterday, has new features and new data related to the use of model organisms in understanding the genetic and genomic basis of human biology, health and disease. Salient features of the 3.0 release include new allele pages with variant and transcript data, new disease models on gene and disease pages, data files available for download, etc. To learn more about the latest features and data, check out the release notes.

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













WS264 release
 

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C. elegans sORFs


sORFs.org is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq).


It contains predicted sORF regions for several species, including C. elegans.


We have annotated 118 predicted sORF regions as coding (CDS) isoforms of the existing genes. It is likely that in the next release, where these isoforms do not overlap with existing isoforms, these sORF regions will be changed to be individual genes and not isoforms.


52 of these annotated sORF regions do not start with the canonical Methionine AUG initiation codon. It is possible that they use a non-canonical initiation codon. Some of these non-canonical initiation codons are not the expected non-canonical initiation codon Isoleucine, but code for residues like Valine.


Trichuris muris


This release we see the integrated of the Edinburgh strain of Trichuris muris version TMUE3.1. This species has been fully integrated as a core species meaning there are stable IDs and tracking with inclusion in all additional pipelines and analysis.

The genome assembly and gene annotation has been taken directly from the Pathogen Genomics group at the WTSI. Additional mapping of gene mergers, splits and transfer of IDs from the TMUE2.2 has been done to allow users to identify their genes of interest.


Caenorhabditis nigoni


This release includes the Caenorhabditis nigoni genome assembly and gene set described in “Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins” by Da Yin, et. al (Science 359,55-61 2018) as non-core species set.

This species should be of special interest, due to its phylogenetic closeness to C.briggsae and its differences in sexual reproduction.


The data is available as files on the WormBase FTP site, as well as the JBrowse genome browser.