Gene Transfer Format (GTF) files now available

WormBase now provides the canonical gene set for each species in Gene Transfer Format (GTF, These files can be used directly by a number of popular sequence analyses tools (e.g. Cufflinks).

The GTF files are available from the WormBase FTP site, for example, the GTF file for C. elegans, c_elegans.PRJNA13758.WS253.canonical_geneset.gtf.gz, is available here.


WS247: C. briggsae genes have descriptions!

In the previous WS246 release we introduced automated gene descriptions for C. elegans genes that lacked a manually written one. These gene descriptions include information related to orthology, process, function and sub-cellular localization (when these data-types have been curated in the WormBase database), giving the user a quick overview of the gene. The current WS247 release includes automated descriptions for over 18,000 C. briggsae genes.  Check out the C. briggase gene pages to view these descriptions under ‘Overview’!  In future releases, we will add genes from many more species!  Also, WormBase is working on user-friendly forms which you can use to edit these descriptions and make them better.

WormBase release WS247

Orthology update

* Data from Inparanoid was updated to version 8
* Orthology data for all core nemtatodes and model organisms was imported from WormBase Parasite release 1
* OMA and TreeFam data was removed in preparation for an update (TreeFam accessions will remain as database crossreferences)

Expression and Picture update

* A large set of expression graphs for other nematodes produced by Yanai’s has been added

RNASeq data

The RNASeq data will become richer in WS247.

There will also be “control” mean and median FPKM values derived from the data which does not have a specific experimental condition applied.

New/updated reference genomes

This release we see a rebuild of C. elegans, B. malayi and O. volvulus. Various data classes and curational activites have been undertaken on these species since the release of WS246

Announcing WormBase ParaSite

Parasitic worms (helminths) are responsible for more than a billion human infections globally and have a devastating impact on livestock and agriculture. As international efforts to sequence the genomes of parasitic helminths gather pace, the WormBase groups at EMBL-EBI and Wellcome Trust Sanger Institute have collaborated on the creation of a new BBSRC-funded resource, WormBase ParaSite, to analyse, store and present information on these genomes. WormBase ParaSite is closely integrated with and complementary to the main WormBase web-site, the central mission of which is to support researchers using Caenorhabditis elegans as a model system.

The first release of WormBase ParaSite includes annotated genomes from 82 species (57 nematodes and 25 platyhelminths), with features including:

  • A genome browser for every genome
  • Comparative analysis (gene orthology and paralogy) using the Ensembl Compara Gene Tree inference method
  • Full text and sequence search (BLAST) services

Development in the coming months will see improved cross-linking to and from the main WormBase site, incorporation of new genomes and data sets, and new querying interfaces and tools oriented towards the use-cases of parasitologists.