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!

WS249: reorganization of parasitic non-core species

Starting with the WS249 release of WormBase we will point users to the new WormBase ParaSite portal for parasitic nematodes that are not curated as part of the WormBase core species.

Species that can now be found at WormBase ParaSite are:
Ancylostoma ceylanicum (PRJNA231479|PRJNA72583)
Ascaris suum (PRJNA62057|PRJNA80881)
Bursaphelenchus xylophilus (PRJEA64437)
Dirofilaria immitis (PRJEB1797)
Haemonchus contortus (PRJEB506|PRJNA205202)
Loa loa (PRJNA60051 )
Meloidogyne hapla (PRJNA29083)
Meloidogyne incognita (PRJEA28837)
Necator americanus (PRJNA72135)
Trichinella spiralis (PRJNA12603)
Trichuris suis (PRJNA179528|PRJNA208415|PRJNA208416)

Introducing a new genome browser for WormBase

JBrowse

We are pleased to introduce a new genome browser that we are currently testing as a replacement for the current, long serving genome browser (GBrowse). The new browser, an implementation of JBrowse from the GMOD project, is currently available at at http://www.wormbase.org/tools/genome/jbrowse.  The new genome browser has a fast and pliable user interface; becoming oriented to the new browser should be relatively painless as it shares many design features in common with the current browser.

The new genome browser also has new functionality not available in the old one.  Key among these are (all of which are available from the genome browser’s file menu):

  1. Opening many types of data files (GFF, BAM, BigWig/BigBed, VCF), without having to upload them (so it’s *fast*).
  2. Creating combination tracks, where the contents of any two tracks can be combined using set or arithmetic operations.
  3. Making a sequence (DNA or amino acid) search track that will highlight when a motif is present (the search string can take the form of regular expressions–please let us know if you’d like help writing a regular expression).

Other useful features include the ability to “pin” a track to the top of the browser so it won’t scroll off the top of the page (simplifying visual comparisons with other open tracks), and a “full page” button that will open a new browser window where the genome browser takes up the full page.

Please try out the new browser and give us any feedback you can think of, either things you’d like to see, things you don’t like, whatever.

WS249: Parasite Papers II

For the upcoming WS249 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Rateb ME, Yang D, Vodanovic-Jankovic S, Yu Z, Kron MA, Shen B.Adipostatins A-D from Streptomyces sp. 4875 inhibiting Brugia malayi asparaginyl-tRNA synthetase and killing adult Brugia malayi parasites. J Antibiot (Tokyo). 2015

Referenced Genes: Bma-nars-2

Yang Y, Wen Yj, Cai YN, Vallée I, Boireau P, Liu MY, Cheng SP.Serine proteases of parasitic helminths. Korean J Parasitol. 2015 Feb;53(1):1-11.

Referenced Genes: Bm10893, Bm4862, OVOC9258, OVOC9605

O’Connell EM, Bennuru S, Steel C, Dolan MA, Nutman TB.Targeting Filarial Abl-like Kinases: Orally Available, Food and Drug Administration-Approved Tyrosine Kinase Inhibitors Are Microfilaricidal and Macrofilaricidal. J Infect Dis. 2015 Feb 5.

Referenced Genes: OVOC2839, Bm3303, Bm3304