WormBase ParaSite is recruiting

We are seeking a talented bioinformatician to work on a wide range of analysis, integration, production and community-engagement activities for WormBase-ParaSite, and also actively participate in the exciting next phase of development for the resource.

Application closes 15th October 2015.

Further details and application on the Wellcome Trust Sanger Institute website

Nobel Prize for work on parasitic nematodes

We would like to congratulate William C Campbell and Satoshi Ōmura to their joint nobel prize in Physiology or Medicine, which they received for their discovery of Avermectin and further development into Ivermectin, which is widely used in anthelmintic therapy of Loa loa and Brugia malayi infections.

The prize is shared with Youyou Tu, who received the other half for her work on novel malaria treatments based on active ingredients of Artemisia annua.

Reference: “The Nobel Prize in Physiology or Medicine 2015″. Nobelprize.org. Nobel Media AB 2014. Web. 5 Oct 2015.

Announcing WormBase ParaSite release 3

We are pleased to announce the third release of WormBase ParaSite (http://parasite.wormbase.org), the home for parasitic worm draft genomes and genomic data in WormBase.

This release includes a number of new genomes, data and functionality.  A summary of the updates is outlined in the release notes below.

New genomes
———–
This release includes two new genomes:

  • Loa loa (PRJNA246086)
    Genome assembly and annotation from the Dunning Hotopp group at the University of Maryland, described Tallon et al (2014), PMID:25217238.
  • Echinococcus canadensis (PRJEB8992)
    Genome assembly by the BMHID group at Instituto de Microbiología y Parasitología Médica, University of Buenos Aires, Argentina; and the Genomics and Computational Biology Group of the CPqRR at Oswaldo Cruz Foundation, Belo Horizonte, Brazil.  The work is described by Kamenetzky et al (manuscript in preparation).

New data
———–
RNASeq data for samples from three Cestode species: example region.

Tools update
———–
REST API – From this release, we now provide language-agnostic programmatic access to the data in WormBase ParaSite via a RESTful interface.

New BLAST service – This release includes two important changes to our BLAST service.  Firstly, we have switched from using WU-BLAST to the faster NCBI BLAST+.  Queries may give subtly different results compared with the previous version.  Secondly, we have removed the limit on the number of species that can be searched at once.  This enables a query to be searched against (for example) all nematode genomes.

Please send your feedback to [email protected]

Announcing WormBase ParaSite release 2

We are pleased to announce the second release of WormBase ParaSite (http://parasite.wormbase.org), the home for parasitic worm draft genomes and genomic data in WormBase.

This release includes eight new annotated genomes, taking the total number of nematode and flatworm genomes in WormBase ParaSite to 97, representing 89 species.  The new genomes include:

  • Fasciola hepatica (PRJEB6687)
  • Opisthorchis viverrini (PRJNA222628)
  • Pristionchus exspectatus (PRJEB6009)
  • Five Steinernema genomes, including Steinernema carpocapsae (PRJNA202318)

This release also includes a new data-mining tool, the WormBase ParaSite BioMart (http://parasite.wormbase.org/biomart/martview).  The interface and underlying software for this are based on the Ensembl BioMart, the main difference being that WormBase ParaSite BioMart collects data for all species into a single underlying database. This means that a single query can be used to filter and report data from multiple species at once, for example all species of a given taxonomic clade.

Please send your feedback to [email protected]

Announcing WormBase ParaSite

We are pleased to announce the first release of WormBase ParaSite (http://parasite.wormbase.org), the new home for parasitic worm draft genomes and genomic data in WormBase.

Parasitic nematodes and flatworms (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 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 aligned with and complementary to the main WormBase web-site (www.wormbase.org), 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 integration with main WormBase site, incorporation of new genomes and data sets, and new querying interfaces and tools oriented towards the use-cases of parasitologists.

Please send your feedback to [email protected]