Please note that the WormBase website has been updated to the WS268 release. Details about this release may be found in the Release Notes for WS268. The notes include a list of files that we publish on our FTP site.
New chapter of WormBook in GENETICS
Check out the new chapter of WormBook in GENETICS about mitotic cell division by Lionel Pintard and Bruce Bowerman – ‘Mitotic Cell Division in Caenorhabditis elegans‘.
Paper of Interest: Comparative study of 81 genomes of parasitic and non-parasitic worms
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‘.
Update on protein-protein interaction data in WormBase
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.
New SPELL server: Fresh look and faster
Please note that we have moved the WormBase SPELL tool to a new server on the Amazon Cloud: https://spell.wormbase.org. This should not affect any of our users, as the ‘Tools’ link on the main WormBase menu bar will take you to this new URL.
SPELL (Serial Pattern of Expression Levels Locator) is a query-driven search engine for microarray, RNAseq and Proteomics data. Given a small set of query genes, SPELL identifies which datasets are most informative for these genes, then within those datasets, additional genes are identified with expression profiles most similar to the query set. WormBase SPELL has collected over 6,000 experiments for 9 nematode species. Users can also download these datasets for their own analysis. See WormBase SPELL Tutorial: http://wiki.wormbase.org/index.php/SPELL
The new WormBase SPELL server is twice as fast as the old version. Please give it a try and let us know what you think!