WormBase ParaSite HomeVersion: WBPS19 (WS291)-  Archive: WBPS18
e.g. O. volvulus, PRJNA60051, WBGene00262434, Bma-eat-4, eat-4 or metallopeptidase

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    Release Log

    Version 18.0 (March 2023)

    Genomes

    Functional genomics data
    • New RNASeq pipeline for genome updates. The new RNA-Seq processing pipeline developed by Ensembl Metazoa has been used to process 178 studies for 34 genomes that have had updated assemblies and/or gene models since release 16. This will fix issues with wrongfully aligned jbrowse tracks and outdated gene expression values.
    3D protein structure models from AlphaFold
    • Over 2 million 3D protein structure models from AlphaFold are now available for 239 genomes species. The AlphaFold predicted model (example) is available through the top-left menu on the transcript pages.
    Pairwise Whole Genome Sequencing alignments
    • Whole genome alignments between genomes in the same taxonomic group can be browsed and visualised through the Ensembl Genome Browser "Configure Tracks" functionality. Follow this tutorial to learn how to visualise these alignments. The whole genome alignments are also available for download in HAL file format, through our FTP site.
    Archive Site Tools
    • Updated comparative genomics (orthologs and paralogs) and protein families.
    • Updated BioMart, BLAST and VEP.

    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: 3.0 (30th July 2015)

    Genomes

    • Total: 99 genomes representing 90 species
    New Genomes Updated Annotations RNA-Seq Alignments

    Transcriptomic data tracks now available for three cestode species:

    Tools

    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