We are thrilled to announce the release of WormBase ParaSite 18 (WBPS18), the resource’s most comprehensive update yet, with the largest number of new genomes and updated annotations since its first launch. WBPS18 hosts 240 different genomes from 181 species.
In WBPS18, users can now browse and visualise whole genome alignments between genomes in the same taxonomic group. Cactus, a next-generation aligner that stores whole-genome alignments in a graph structure, was utilised to calculate multiple pairwise genome alignments between WBPS genomes. These genomes have been assigned to 5 big taxonomic groups, and pairwise alignments can be viewed between the genomes of each group.
These alignments are viewable through the Ensembl Genome Browser. Follow this tutorial to learn how to browse these alignments.
The whole genome alignments are also available for download in HAL file format, through WBPS FTP site.
In July 2022, AlphaFold predicted structures for almost every catalogued protein known to science.
In release 18, WormBase ParaSite incorporated these models. Now, over 2 million 3D protein structure models from AlphaFold are available for 239 genomes species. The AlphaFold predicted model (example) is available through the top-left menu on the transcript pages.
Follow this tutorial to learn how to browse your favourite protein models in WormBase ParaSite.
From release 16, due to the retirement of the RNASeq-er API, RNASeq data of genomes that had assembly or annotation updates were not re-aligned. For 34 updated genomes (releases 16 and 17), this affected their RNA-Seq alignment tracks available on the Ensembl Browser, Jbrowse and their gene counts on the Gene expression platform.
For this release, the novel RNA-Seq pipeline developed by the Ensembl Metazoa group has been utilised to re-align the RNA-Seq data for these 34 genomes. The pipeline is using HISAT2 to perform the read alignments and htseq-count to count reads in features.
If you would like a new gene expression study to be included, please contact WBPS.
The previous WormBase ParaSite Release 17 has been archived and remains accessible here.
If you’re using WormBase ParaSite, then you should subscribe to the resource’s mailing list so you can frequently receive updates on WormBase Parasite new releases, like this one, new features, career opportunities, and upcoming conferences and workshops.
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