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!

 

WS267 release of 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.

WormBook in GENETICS

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!

Best,
Iva

WS266 release

Please note that the WS266 version of WormBase has been released! The release notes for this release describe the data types and their numbers. A list of all files available on our FTP site can also be viewed.  Changes in this release include the following:

Physical Interaction data curation

We have added over 5000 manually curated physical interactions which include binary protein-protein interactions as well as protein interactions that occur in a protein complex. Protein-protein interaction data can be found as a part of physical interaction data in the Interactions widget on the gene page. The Interactions widget provides different types of interaction data related to the gene of interest, such as physical, genetic, regulatory, and predicted interactions.

 

Protein Identifiers

We have made a change to our internal identifiers for nematode protein sequences. Previously, we prefixed each identifier with *two* prefixes to denote which  species the protein is from, e.g. WP:CE00001. We have removed the first prefix (the “WP:”) from these identifiers.

Since these prefixes are almost entirely invisible on the site and have never been used by external resources hosting worm data (e.g. UniProt), this change should not affect most users.