New & Noteworthy
February 25, 2011
In an effort to provide a comprehensive view of all of the sequence-based functional elements in the Saccharomyces cerevisiae genome, SGD will collect sequence-based functional feature annotations from published datasets, aimed at charting the yeast transcriptome (e.g. protein-coding genes, non-coding RNAs), chromatin landscapes (e.g. nucleosome phasing, histone modifications and variations), as well as cataloging regulatory sequence elements (e.g. transcription factor binding sites, splicing signals) and more.
We have upgraded our GBrowse genome viewer to allow users to quickly and easily browse this information-rich view of the yeast genome. In addition, 17 new data tracks have been added, including recent surveys of the budding yeast transcriptome (Nagalakshmi et al. 2008; Xu et al. 2009; Yassour et al. 2009) and catalogs of regions favored for recombination and replication events (Mancera et al. 2008; Buhler et al. 2007; Xu et al. 2006; Eaton et al. 2010). We invite authors to work with us to integrate their data into our GBrowse viewer pre- and/or post-publication as we move forward. Watch for the regular addition of new tracks to SGD’s GBrowse in the future! Please contact us if you are interested in participating or have questions and comments.
February 23, 2011
Expression analysis at SGD has a new powerful interface and many new datasets. The new interface uses a tool called SPELL (Serial Pattern of Expression Levels Locator). This analysis tool facilitates the rapid identification of the most informative datasets and co-expressed genes based on patterns of expression shared with the query gene(s). By transitioning to this tool, expression data from a comprehensive collection of almost 400 datasets are now available at SGD. The expression analysis tool can be accessed via the expression tab, the expression summary histogram, and in the functional analysis pulldown located on Locus Summary pages. These new data and the SPELL interface have been provided through a collaboration with the SGD Colony at Princeton University. Thanks to Peter Koppstein, Lance Parsons, and Kara Dolinski for help with data preparation and implementation of SPELL at SGD. SPELL was developed by the Troyanskaya lab at Princeton University (Hibbs et al. (2007) Bioinformatics 23:2692).
February 18, 2011
SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.
February 15, 2011
SGD’s Batch Download tool will be retired soon, because all of its functions and many more can now be accomplished via YeastMine, which offers flexible queries and fast retrieval of multiple datatypes from SGD for a custom list of genes or proteins. Please contact us if you have any concerns.
February 15, 2011
YeastMine, a powerful data search and retrieval tool, has been upgraded to InterMine version 0.95. This software update includes many new features, improvements and bug fixes. Key new features include a completely redesigned homepage, a more powerful multifaceted keyword search and template ranking by frequency of search. YeastMine queries multiple datatypes: chromosomal features, protein features, GO annotations, phenotypes, interaction data and curated literature. YeastMine will soon replace several search tools at SGD. Please explore its powerful query options and send us feedback.
YeastMine was created through an NIH funded collaboration between InterMine, the Rat Genome Database (RGD), and the Zebrafish Model Organism Database (ZFIN) to provide interoperability between model organism databases.