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SGDTM is a scientific
database of the molecular biology and genetics of the yeast
Saccharomyces cerevisiae, which is commonly known as baker's
or budding yeast.
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New and Noteworthy |
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Follow the Poland yeast meeting on Twitter!
- July 12, 2011
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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!
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SGD Curation News |
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Textpresso now includes publications from 2011
- June 21, 2011
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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.
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New Genome-wide High-throughput Data Tracks Added to GBrowse and PBrowse
- June 09, 2011
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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.
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25th International Conference on Yeast Genetics and Molecular Biology, Poland
- May 3, 2011
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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.
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SGD Quarterly Newsletter
- May 5, 2011
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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.
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Expanding the View of the Functional Budding Yeast Genome
- February 25, 2011
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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.
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New Expression Analysis Tool and Datasets
- February 23, 2011
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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).
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Previous New and Noteworthy items are listed in
What's New in SGD in 2011?
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Find SGD Pages: |
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The Saccharomyces Genome
Database (SGDTM) project is supported
by a P41 grant, National Resources [HG001315], from the
National Human Genome Research
Institute at the US National
Institutes of Health. The SGDTM project is located in the Department of Genetics at the
School of Medicine,
Stanford University. The
trademark on SGDTM is held by The
Board of Trustees, Leland Stanford Junior University.
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