New & Noteworthy
December 16, 2011
Expression analysis at SGD now offers the ability to filter datasets by condition(s) or process(es) studied. A set of controlled vocabulary (CV) terms describing various perturbations associated with microarray experiments has been constructed and defined, and these terms have been used to tag the comprehensive collection of almost 400 datasets now available in SGD’s instance of SPELL (Serial Pattern of Expression Levels Locator). In this manner, datasets displayed in search results can be filtered using tags (CV terms) such as “oxidative stress” or “sporulation.” Filtering is an option for the “New Search,” “Show Expression Levels,” and “Dataset Listing” features. The SPELL interface has been provided through a collaboration with the SGD Colony at Princeton University. Special thanks to Peter Koppstein, Lance Parsons, and Kara Dolinski for help in implementing the dataset tag filtering option for SPELL at SGD.
November 15, 2011
YEASTBOOK is now available in the November 2011 issue of GENETICS. This month’s issue includes a Perspectives article by David Botstein and Gerry Fink, a review about transcriptional regulation written by Steve Hahn and Elton Young, and a review about sporulation written by Aaron Neiman. Edited by Alan G. Hinnebusch, YEASTBOOK will be a compendium of comprehensive reviews that provides the current state of knowledge of the molecular biology, cellular biology, and genetics of Saccharomyces cerevisiae. Approximately 50 YEASTBOOK review articles will be published in GENETICS (a peer-edited journal of the Genetics Society of America) over the next two years. Gene names mentioned in YEASTBOOK reviews are linked back to SGD.
Read an editorial by Alan Hinnebusch and Mark Johnston to find out more about YEASTBOOK.
October 3, 2011
SGD now has available ORF DNA and protein sequence alignments for dozens of S. cerevisiae strains. The alignments are accessible via a new ‘Analyze Sequence’ section on the Locus Summary pages. Also available are retrieval and download options. Stay tuned in the coming months as SGD continues to develop additional tools for viewing and analysis of these sequences.
September 20, 2011
SGD is developing a library of short video tutorials designed to step you through using various SGD tools. Check out those currently available for YeastMine, GBrowse, and SPELL, located on our SGD Video Tutorials page. Preview the “YeastMine is Awesome” video below, describing just a few of the “awesome” things you can do in YeastMine!
September 15, 2011
SGD has upgraded Yeast Biochemical Pathways (YeastCyc) to Pathway Tools Version 15.0. This version gives the pathway database a new look and offers new features for querying and analyzing data. A pathway-specific toolbar, available on each pathway web page, provides easy navigation and new features, including options to highlight pathways and substrates on the cellular overview and to download a list of genes from a specific pathway. Pathway files (yeastcyc15_201109.tar.gz and biochemical_pathways.tab) can be downloaded from SGD’s downloads page.