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.
Categories: Data updates, Website changes
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.
Categories: Tutorial
October 03, 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.
Categories: Sequence
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!
Categories: Tutorial
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.
Categories: Website changes
September 06, 2011
SGD has updated both its BLAST Search and Pattern Matching (PatMatch) tools to include genomic, coding, and protein sequences from 26 additional S. cerevisiae strains. Look for more updates and tools from SGD for analyses of the S. cerevisiae strain genomes in the coming months.
Categories: Sequence, Website changes
September 01, 2011
SGD has updated its file Downloads Site. The new look includes complete genomic and protein sequence files for the current S288C reference sequence (Release 64) and all previous releases. Genomic sequence and annotation for numerous S. cerevisiae strains are also available for download. As always we make available many other published datasets and a large collection of information curated by SGD from the literature.
Categories: Website changes
August 22, 2011
SGD’s “Advanced Search” and “Batch Download” tools will be retired on August 31st. All of the functions of these tools, plus many more, can be accomplished by YeastMine, which offers flexible queries and fast retrieval of multiple datatypes from SGD for a custom list of genes or proteins.
Short video tutorials that walk you through some of the basic actions in YeastMine are also available.
Categories: Website changes
August 17, 2011
Dear Colleagues and Friends,
The 25th International Conference on Yeast Genetics and Molecular biology, has ended. It was a great success and an opportunity to attend very interesting and inspiring lectures given by distinguished speakers as well as to listen to exciting workshop and poster presentations. We hope you enjoyed your stay in Olsztyn despite the unsteady weather and mosquito bites. We hope you met your friends and made new friendships, as we did. We hope to see you again in Frankfurt.
Until then, to keep the memories alive, please visit the Conference on-line photo album holding over 700 photos you can view on-line and also download freely.
Sincerely, Joanna Rytka and the Organizing Team
Categories: Conferences
August 12, 2011
SGD has updated its Yeast Molecular Function and Biological Process GO Slims to include additional terms. The Yeast GO Slims are a set of GO terms that best represent the major biological processes, molecular functions, and cellular components that are found in S. cerevisiae. GO Slim terms are useful in mapping precise, “granular” gene annotations to more general “high-level” terms. These terms have been selected by SGD curators based on annotation statistics and biological significance. To complement the expanded Yeast GO Slims, we have also added “generic GO-Slim” options to our GO Slim Mapper tool. The generic GO-Slim is developed and maintained by the Gene Ontology Consortium and includes fewer and higher-level terms than those provided by the Yeast GO-Slim.
The Yeast GO Slims are available for analysis via the GO Slim Mapper tool and YeastMine. Mapping of all the yeast gene products to the Yeast GO Slims is also available as a graphical view on the Genome Snapshot page and via the go_slim_mapping.tab file on the downloads site.
Categories: Data updates