ParaSite Release 3

We are pleased to announce the third release of WormBase ParaSite, the home for parasitic worm draft genomes and genomic data in WormBase.

This release includes two new annotated genomes, taking the total number of nematode and flatworm genomes in WormBase ParaSite to 99, representing 90 species. The new genomes are:

  • Echinococcus canadensis (PRJEB8992)
  • Loa loa (PRJNA246086)

This release also includes a REST API, providing language-neutral programmatic access to ParaSite data via a RESTful interface (http://parasite.wormbase.org/api/), and an improved BLAST search which is faster and has no limit on the number of species that can be BLASTed against (http://parasite.wormbase.org/Tools/Blast).

Finally, in this release we are displaying tapeworm RNASeq data for the species Echinococcus granulosus, Echinococcus multilocularis and Hymenolepis microstoma (as example). We will be including more transcriptomic data sets in upcoming ParaSite releases so if you would like to suggest datasets you would like to see displayed please get in touch!

WormBase ParaSite release 2: more genomes and new data-mining tool

We are pleased to announce the second release of WormBase ParaSite, 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. 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.

    Parasite Focus – BigWig External Annotations

    This is an example of attaching an external annotation file to the ParaSite browser.

    As annotation, we will use a BigWig file containing a PhyloP profile of the Trichinella spiralis genome, which is available here. In addition we need to put it onto a public accessible HTTP server.

    We will use BigWig as format, as the size of WIG files is limited to 5MB, which would only cover parts of the Trichinella spiralis genome (as the format contains a score for each base pair).

    Disclaimer: this data is just an example and should not be used for a in depth study of conservation

    We will start at the ParaSite main page and choose Trichinella spirlalis
    ParaSite main page

    From there we should end up on a species specific page, where we can search for, as example, EFV62134 (which is a INSDC identifier of an T.spiralis gene)
    T.spiralis main page

    This will return a gene page, which includes a genome track to which we can attach our annotation.
    example gene page for T.spiralis

    We can also switch to the genome location view and attach it there (but note: if you want to see it on both, you need to attach it to both)
    example genome location view

    both should contain a “Manage Your Data”, which we will use to attach the bigwig file using the “add custom track” link at the bottom of the view
    data management view

    from there we will pick “Trichinella spiralis” as genome, “BigWig” as file format and put “http://www.ebi.ac.uk/~mh6/tspiralis.phylop.wib” into the URL (which you potentially need to change to wherever you host it from).
    data details view

    You can also pick the colour scheme (the examples below use the cyan one) and then you should get on the gene view something like that
    PhyloP track for EFV62134

    and for the location view, respectively that
    location view PhyloP

    It is also possible to change the display of the track by clicking on the gear shaped icon next to it.