WormBase is happy to announce that weāve released a new version of the Author First Pass (AFP) form.Ā Weāve improved our methods for identifying relevant genes and alleles and added an FAQs section to help guide you through the process.Ā Full details are available in theĀ V2 Release Notes.Ā Thank you for your participation and feedback; we look forward to seeing your future submissions!
The URL for the V2 Release Notes link is:Ā Ā https://github.com/WormBase/author-first-pass#release-notes
WormBase updates in WS277 – new protein schematic images!
We have released the 277th version of WormBase! As always, for a detailed report please look at the WS277 release notes.
New features: Weāve updated the protein schematic image in the homology widget on protein pages (see, for example, theĀ UNC-2, isoform aĀ page.) This image displays protein domains and exons mapped to amino acid coordinates, making it easy to see which regions of a transcript correspond to specific features. Driven by JBrowse ā the genome browser at WormBase ā users can click through the image to an interactive view in amino acid coordinates. From that familiar interface, one can scroll, export sequence (can they?), get additional information on specific features, and zoom in to single amino acid residue resolution, color-coded by chemical property.Ā The previous static protein schematic image remains available by clicking on the āLegacy Protein Schematicsā link, but will be removed after the WS278 release.
New data sets:
C. elegans: Additional Nanopore transcript data has been added.
C. elegans VC20210: The VC2010 strain data includes gene annotation which has been manually curated to improve the coding gene structures lifted over from the N2 strain annotation. This process is substantially complete, with some work still to be done on chromosome X. The number of coding genes which do not map correctly has been reduced so far from around 400 down to 50 genes which cannot yet be located and 10 which appear to be pseudogenes in VC2010. There are 20 genes which appear to be duplicated in N2 and have disappeared in VC2010. There have been 39 novel coding genes created.
Check out Venn diagrams for interaction data in WormBase
WormBase curates four different types of gene-to-gene interaction data: genetic, regulatory, physical, and predicted. These data are found in the interactions widget in each gene page. Aside from the predicted interactions, the other three types are curated with direct experimental evidence from the literature. Check out the micropublication which describes the Vennter tool. This tool is integrated into the interactions widget on WormBase gene pages and allows the visualization and analyses of interaction data.
Textpresso for coronovirus
Announcing the special edition of Textpresso covering coronavirus literature– it contains 31,000 articles from the PMC open access archive.
SimpleMine now includes protein domains
SimpleMine can now be used to obtain protein domains for a list of genes. You can select one or several attributes from a list, such as Gene ID, expression pattern, RNAi phenotype, allele phenotype, etc. Note that all attributes remain selected by default.