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.
Check out the new chapter in WormBook, GENETICS: ‘Caenorhabditis elegans Gastrulation: A Model for Understanding How Cells Polarize, Change Shape, and Journey Toward the Center of an Embryo‘ by Bob Goldstein and Jeremy Nance.
Textpresso is a powerful full text search engine for several biomedical literatures. Textpresso searches are now available on many types of pages in WormBase such as gene pages, variation/allele pages, molecule/chemical pages, etc., in the References widget. Note that you should have the ‘References’ widget open (by clicking on it) from the side bar on a gene, allele, or molecule page. Click on the ‘Textpresso’ link in ‘Find references identified by Textpresso’ at the bottom of the references to trigger a search for that entity by the Textpresso search engine. For example, clicking this link in the ‘References’ widget on the lin-10 page will trigger a full text search by the Textpresso search engine for lin-10 in the C. elegans literature and return a page displaying the search results.
Please note that WormBase version WS274 was released and is the current release now live on the website. The version of the C. elegans reference genome in this release is WBcel235, included since WS235.
Highlights of this release include:
- Isoseq data which was presented at the PacBioNorth America User Group meeting. We applied the PacBio post processing pipeline as described here. The resulting sequences are including in the transcript alignments and will be visible on the genome browser. They will also be included in our automatic transcript generation pipeline in a future release of WormBase.
- Improved code to generate non-redundant transcripts. Each CDS should now have only unique transcripts.
- Improved interaction data display in the Interactions widget: New Venn diagram for the different types of interactions-physical, genetic and regulatory.
For a complete and more detailed list of changes for this release please see:
Check out the new chapter in WormBook, GENETICS, ‘Biology of the Caenorhabditis elegans germline stem cell system‘ by Jane Hubbard and Tim Schedl.