Check out the paper ‘Comparative genomics of the major parasitic worms’ in Nature Genetics by the International Helminth Genomes Consortium and the ‘News and Views’ article by Paul Sternberg, ‘Opening up a large can of worms‘.
Currently WormBase contains over 28,000 physical protein-protein interactions of which 1,500 protein-protein interactions have been curated by BioGRID as a collaboration with WormBase. Within the data set, over 17,000 protein-protein interactions are unique, and over 6,000 unique genes are involved in these interactions. In WormBase, protein-protein interaction data can be found as a subclass of physical interaction data in the ‘Interactions widget’ on the gene report page. The interactions widget provides all types of interaction data related to the gene of interest, such as physical, genetic, regulatory, and predicted interactions. Check out the micropublication ‘2018 Update on Protein-Protein Interaction Data in WormBase‘ by Jae Cho et al., and learn more about this data type in WormBase.
Please note that the WS267 release of WormBase is now live. The complete release notes for WS267 can be viewed here. Some of the highlights include–
Trichuris muris update
Trinity assembled RNASeq reads from publicly available short read data at SRA have been added to Trichuris muris as additional track and alignments. In addition IsoSeq data from long-range PacBio data (provided by the Berriman lab), corrected by genome alignment has been used as additional source to build transcript models.
In addition the Trichuris muris ncRNA gene set has increased from 26 to 759 following the integration of data produced by the WormBase Parasite ncRNA prediction pipeline. These transcripts have been fully integrated with stable IDs and associated naming and meta data.
Gene descriptions for T. muris will be coming in the WS268 release of WormBase.
Brugia malayi update
New gene models provided by the Beech lab for Parasitology at the McGill University have been merged into the official gene set.
From Iva Greenwald:
Three years ago, I announced in this column the creation of WormBook in GENETICS, thanks to a generous funding commitment to our community by the Genetics Society of America.
Please look at what we’ve done so far and you’ll see what a great resource it is: http://www.genetics.org/content/wormbook
We are really hitting our stride now, and you will see WormBase announcements of new chapters increasing apace. The more you demonstrate the value of WormBook through viewing, downloading, and especially, citing the articles, the more the GSA will understand the value of their sponsorship and be inclined to continue it.
Thanks very much!