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!

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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)

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Introducing a new genome browser for WormBase

July 20, 2015
Thumbnail image for Introducing a new genome browser for WormBase

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 […]

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WS249: Parasite Papers II

July 20, 2015

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 […]

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WS249: Parasite Papers I

July 13, 2015

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. Winter AD, Weir W, Hunt M, Berriman M, Gilleard JS, Devaney E, Britton C.Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are […]

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Presentations for IWM WormBase Workshops now available

June 29, 2015

We’ve posted presentations from the WormBase workshops at last week’s International Meeting. SlideShare Dropbox FTP

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WormBase HUBs

June 25, 2015

As shown during the WormBase Workshops of the International Worm Meeting 2015 at UCLA: (Slides/Notes of the WormBase ParaSite / HUBs section) To enable use of up to date data on external sites, WormBase is providing with each release (starting with WS248), selected annotations and comparative tracks as assembly hubs. there are currently two types […]

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Introductory chapter added to WormBook

June 19, 2015

Dear WormBook reader, We are very happy to announce that A Transparent Window into Biology: A Primer on Caenorhabditis elegans, by Ann Corsi, Bruce Wightman, and Marty Chalfie, has just been added to WormBook as a co-publication with GENETICS. This concise and comprehensive review, which serves as an introductory chapter to WormBook, discusses the basic […]

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Nuclear receptor chapter updated in WormBook

June 15, 2015

Nuclear receptor signal transduction in C. elegans, by Adam Antebi, has just been published in the Signal transduction section of WormBook. This chapter updates his 2006 chapter, Nuclear hormone receptors in C. elegans. The updated chapter discusses the role of nuclear receptors as regulators of life history, cell fate, and organogenesis, and their function in […]

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WormBase release WS248

June 8, 2015

The newly released WS248 version of WormBase includes several updates based on curation topics as well as synchronisation with other databases. In addition the use of Gene Ontology has been extended. microRNA update for Brugia malayi The newest data on Brugia malayi microRNAs from miRBase Release 21 has been integrated, which includes pre-miRNA and mature […]

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