WormBase ParaSite HomeVersion: WBPS17 (WS282)

Release Log

Version 17.0 (July 2022)

Genomes

Functional genomics data
  • 200+ RNASeq studies across 95 species.
3D protein structure models for 8 genomes Phenotype data
  • Over 350,000 imported gene-phenotype associations for C. elegans and Schistosoma mansoni, which are also propagated between orthologues for all Wormbase Parasite species, are now availabe to download from the FTP directory.
Gene Name Synonyms
  • Gene name synonyms are now exportable via BioMart BioMart.
Archive Site Tools
  • Updated comparative genomics (orthologs and paralogs) and protein families.
  • Updated BioMart, BLAST and VEP.

Version 16.0 (September 2021)

Genomes

Functional genomics data
  • 160 RNASeq studies across 53 species.
Phenotype data
  • Over 350,000 C. elegans gene-phenotype associations have been imported from our sister site, Wormbase. These gene-phenotype associations have also been propagated between orthologues for all Wormbase Parasite species.
Gene Name Synonyms Archive Sites
  • Introduced new archiving service, making previous WormBase Parasite releases accessible: Release 15 Archive Site.
Feature Updates
  • Deprecated CEGMA scores.
  • Introduced a new BUSCO metric for each genome, based on its genome annotation.
  • Updated repeat feature modeler.
Tools
  • Updated comparative genomics (orthologs and paralogs) and protein families.
  • Updated BioMart, BLAST and VEP.

Version 15.0 (October 2020)

Genomes

Functional genomics data
  • 164 RNASeq studies across 48 species
  • 1 RNAi study
Tools
  • Updated comparative genomics (orthologs and paralogs)
  • Updated BioMart, BLAST and VEP

Version 14.0 (August 2019)

Genomes

Data on gene expression
  • Total: 201 RNASeq studies across 48 species
  • S. mediterranea studies align to the new assembly (ASM260089v1)
Tools
  • Updated Comparative genomics (orthologs and paralogs): removed 7 genomes which have better alternatives
  • Updated BioMart, BLAST and VEP

Version 13.0 (April 2019)

Genomes

Data on gene expression
  • 120 RNASeq studies across 46 species
  • Studies listed per species, with data available for download
  • Subset of the data shown on the species page
Tools
  • Updated Comparative genomics (orthologs and paralogs)- E!95 pipeline using an HMM library for clustering
  • Updated BioMart, BLAST and VEP

Version 12.0 (December 2018)

Genomes

Support for archived IDs
  • Imported prior history of 7 genomes of non-WormBase core species that underwent annotation update
  • Previous identifiers now searchable on the site
  • Visualization of history available on gene pages
Tools
  • Updated Comparative genomics (orthologs and paralogs)
  • Updated BioMart, BLAST and VEP

Version 11.0 (August 2018)

Genomes

Genome Browser Annotation Tools
  • New feature: user comments on gene pages
  • Updated Comparative genomics (orthologs and paralogs)
  • Updated BioMart, BLAST and VEP

Version 10.0 (March 2018)

Genomes

  • Total: 138 genomes, representing 118 distinct species
  • New species: Diploscapter coronatus (PRJDB3143), Diploscapter pachys (PRJNA280107), Caenorhabditis nigoni (PRJNA384657), Parascaris univalens (PRJNA386823)
  • Updated genomes and annotation for: Ascaris suum (PRJNA62057), Echinococcus canadensis (PRJEB8992), Schistosoma haematobium (PRJNA78265), Pristionchus pacificus (PRJNA12644)
  • WormBase core species updated to release WS263
Tools
  • Updated Comparative genomics (orthologs and paralogs)
  • Updated BioMart, BLAST and VEP

Version 9.0 (April 2017)

Genomes

  • Total: 134 genomes, representing 114 species
  • New species: Ditylenchus destructor (PRJNA312427) and Taenia saginata (PRJNA71493)
  • Additional new assembly for Taenia asiatica (PRJNA299871)
  • WormBase core species updated to release WS258
Tools
  • New alternative genome browser (JBrowse) available for all genomes
  • Updated comparative genomics
  • Updated BioMart, BLAST and VEP

Version 8.0 (December 2016)

Genomes

  • Total: 131 genomes representing 112 species
  • New species: Globodera rostochiensis (PRJEB13504) and Gyrodactylus salaris (PRJNA244375)
  • New higher quality assembly for Heligmosomoides polygyrus (PRJEB15396)
  • WormBase core species updated to release WS256
Tools
  • Updated BUSCO scores using version 2 of the software and either the Nematoda or Metazoa lineage as appropriate
  • Updated assembly statistics widget
  • Updated comparative genomics
  • Updated BioMart, BLAST and VEP

Version 7.0 (August 2016)

Genomes

  • Total: 128 genomes representing 110 species
  • 16 new Trichinella genomes: genomes of 12 Trichinella species, including 5 different strains for T. pseudospiralis
  • New genomes for Echinnococcus granulosus (PRJNA182977), Toxocara canis (PRJNA248777) and Wuchereria bancrofti (PRJNA275548)
  • Updated annotation for Onchocerca ochengi (PRJEB1204)
  • WormBase core species updated to release WS254
  • Macrostomum lignano included in comparative genomics analysis
Genome Browser Annotation
  • New RNASeq tracks for Brugia malayi, Fasciola hepatica and Trichuris muris
  • New variation tracks imported from European Variation Archive for Schistosoma mansoni and Strongyloides ratti
  • Community annotation track for Stronyloides stercolaris
Tools
  • CEGMA and BUSCO scores calculated for all genomes
  • Assembly statistics widget on species information page
  • Species list now sortable, searchable and exportable
  • Baseline gene expression from Gene Expression Atlas shown for Schistosoma mansoni

Version 6.0 (April 2016)

Genomes

Genome Browser Annotation Tools

Version 5.0 (January 2016)

Genomes

Help and Documentation
  • A comprehesive set of user guides is now available. A link is available at the top right of every WormBase ParaSite page.
RNA-Seq Alignments
  • New alignments added for WormBase core parasites
Tools

Version: 4.0 (10th November 2015)

Genomes

  • Total: 99 genomes representing 90 species
  • WormBase core parasites updated to release WS250
  • Free living nematode genomes for compara, BioMart and BLAST updated to WormBase release WS250
RNA-Seq Alignments Tools
  • Updated comparative genomics
  • Updated BioMart
  • Changes to web interface, based on user feedback

Version: 2.0 (16th March 2015)

Genomes

  • This release: 8 new genomes
  • Total: 97 genomes representing 89 species
New Genomes Tools

Version: 1.0 (30th September 2014)

Genomes

  • 82 Species
  • 89 Genomes
Tools
  • Genome Browser
  • Comparative Genomics
  • BLAST
  • Variant Effect Predictor
  • Raw Data Downloads

Version: 0.1-beta (3rd June 2014)

Limited pre-release demonstration

  • 16 Species
  • 17 Genomes