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
August 11, 2011
SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. This Summer 2011 newsletter is also available online. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.
Categories: Newsletter
August 09, 2011
Wish you were in Cold Spring Harbor for the Yeast Cell Biology meeting, Aug 16-20? SGD will be live tweeting from CSHL, highlighting topics from talks and posters. Keep up with events at the meeting by following @yeastgenome on Twitter or searching #YCB2011 for all tweets!
Categories: Conferences
August 05, 2011
We have added new data tracks to our GBrowse genome viewer from six publications covering various histone acetylation and methlyation modifications (Guillemette et al. 2011; Kirmizis et al. 2007; Liu et al. 2005 and Pokholok et al. 2005) and the mapping of histone variant H2A.Z (Albert et al. 2007 and Guillemette et al. 2005). We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments.
Categories: New Data
July 12, 2011
Wish you were in Poland for the 25th International Conference on Yeast Genetics and Molecular Biology? SGD is live tweeting from the Poland meeting, highlighting topics from talks and workshops. Keep up with events at the meeting by following @yeastgenome on Twitter or searching #ICYGMB for all tweets!
Categories: Conferences
June 21, 2011
The SGD full-text literature search (powered by Textpresso) has been upgraded and updated to include 58,000 papers. Textpresso now includes the ability to restrict your searches to a subset of PMIDs as well as limit the results to a specific section of a paper. The full-text literature search can be accessed via the Full-text Search link on the home page. Thanks to Arun Rangarajan and Hans-Michael Muller from Wormbase for their help upgrading the software.
Categories: Data updates
June 09, 2011
We’ve added new data tracks to our GBrowse genome viewer from eight publications, including recent surveys of nucleosome occupancy and positioning (Kaplan et al., 2009; Field et al., 2008; Mavrich et al., 2008; Lee et al., 2007); ncRNAs and RNA secondary structures (Lardenois et al., 2011 and Kertesz et al., 2010); and transcription factor and RNA Pol II occupancy (Venters et al., 2011 and Mayer et al., 2010). We have also added a data track to our Pbrowse proteome browser, displaying mature N-termini of mitochondrial proteins as determined by Vögtle et al., 2009. Both GBrowse and PBrowse have been upgraded to the most recent software with several new features.
We invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers pre- and/or post-publication as we move forward. Watch for the regular addition of new tracks to SGD’s GBrowse and PBrowse in the future! Please contact us if you are interested in participating or have questions and comments.
Categories: Data updates, New Data