The data of the latest INSDC submission of the H.bacteriophora annotation project has been added to WormBase.
It is available as flatfiles to download from ftp://ftp.wormbase.org , on GBrowse and as connections to ortholog nematode genes.
Using WormBase 2: remember to open widgets
If you want to see all the data that you were used to seeing on the gene page, remember to open the related widgets on the left sidebar. For example, if you want to see all the alleles/variations of a gene, remember to click on the ‘Genetics’ widget. Once you do this, this preference is remembered.
BLAT search options expanded to all species
Did you know that on the new WormBase website you can now run BLAT nucleotide similarity searches against any of the species housed at WormBase? Just visit the BLAST/BLAT Search page to run your queries.
Caenorhabditis species 5
Caenorhabditis species 5 is a member of the Elegans group of species, which morphologically resembles C. elegans itself and is closely grouped with it evolutionarily (Kiontke et al., 2011). It is a gonochoristic species, requiring mating between males and females for reproduction, and the closest outgroup to the interfertile pair of hermaphroditic C. briggsae and male-female C. sp. 9. Its geographic distribution is remarkably confined to East Asia (Google Maps), being commonly found in China and northern Vietnam, particularly in habitats with moist decaying vegetation. C. sp. 5 shows strikingly high molecular diversity, assayed by SNP variability (Wang et al., 2010); however, its codon usage patterns are similar to those of C. elegans (Cutter et al., 2008).
Cutter A.D., Wasmuth J.D. and Washington N.L. (2008). Patterns of molecular evolution in Caenorhabditis preclude ancient origins of selfing. Genetics 178, 2093-2104.
Kiontke K.C., Felix M.A., Ailion M., Rockman M.V., Braendle C., Penigault J.B. and Fitch D.H. (2011). A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol. Biol. 11,339.
Wang G.X., Ren S., Ren Y., Ai H. and Cutter A.D. (2010). Extremely high molecular diversity within the East Asian nematode Caenorhabditis sp. 5. Mol. Ecol. 19, 5022-5029.
Welcome to the new WormBase website!
We are very excited to present the new version of the WormBase website!
Designed from the ground up to be fast, customizable, and extensible, the new site offers a number of new features. Try out the new full database search with faceted results by both data type and species. Explore the role of human orthologs of worm genes by searching for human diseases. Log in and save favorite items and references that you access frequently. Share your knowledge with the community and WormBase curators by leaving comments.
Some things have been renamed; others rearranged; and still others removed outright. We know it might take some time to become accustomed to the new layout. If you have questions, comments, or suggestions, chat with us when we’re online (see the LiveChat tab on the right hand side of the screen), send us a question using this web form, or just drop us an email at [email protected].
The old version of WormBase will be maintained for the foreseeable future at legacy.wormbase.org, but the databases will be frozen at WS230.
We’ll be updating the site with exciting new features and data on regular basis. These include a new data mining and querying platform, an alert system to notify for updates on your favorite items, and new species.
As always, we welcome your feedback!