New & Noteworthy

Filter Expression Data by Experimental Condition

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

YEASTBOOK now available!

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

Download and Align S. cerevisiae Strain Sequences

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

Short Video Tutorials for Using SGD Tools

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

New Look and Features for Yeast Biochemical Pathways

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

Sequence Data for 26 Additional S. cerevisiae Strains Available

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: Website changes Sequence

SGD Downloads Site Updated

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

Retiring Advanced Search and Batch Download

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

Message from the organizers of the 25th ICYGMB in Olstyn, Poland

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

GO Slims Updated

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

SGD Summer 2011 Newsletter

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

Follow the CSHL Yeast Cell Biology Meeting on Twitter!

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

New Histone Modification and Variant Data Tracks Added to GBrowse

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

Follow the Poland yeast meeting on Twitter!

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

Textpresso now includes publications from 2011

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

New Genome-wide High-throughput Data Tracks Added to GBrowse and PBrowse

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: New Data Data updates

SGD Spring 2011 Newsletter

May 05, 2011

SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. This Spring 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

25th International Conference on Yeast Genetics and Molecular Biology, Poland

May 03, 2011

Registration is open for the 25th International Conference on Yeast Genetics and Molecular Biology. The meeting will take place on July 11-16 in Olsztyn-Kortowo, Poland. Visit the conference website to get more information and to register. SGD is having a workshop on July 12 at 7:30 PM; come learn about new tools and data at SGD.

Categories: Conferences

Expanding the View of the Functional Budding Yeast Genome

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.

Categories: New Data

New Expression Analysis Tool and Datasets

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).

Categories: Data updates Website changes

Next