SGD Quarterly Newsletter
Posted July 20, 2006
In this issue:
- Visit SGD at the Yeast Genetics and Molecular Biology Meeting - Win a T-shirt or Cap
- Search for a Strain Background and more in 44,000+ Yeast-Related Full Text Articles
- View Updates to the Systematic Sequence on New Chromosome History Pages
- Sequence and Annotation Changes Made to the Systematic Sequence of S. cerevisiae
- Transcription Factor Data Remapped to Updated Sequence
- New Summary Paragraphs for 115 Genes and Chromosomal Features
- New Datasets Added
- Community News
Manage your Newsletter Subscription
About this Newsletter
This is the July 2006 issue of the quarterly SGD newsletter. The
goal of this newsletter is to inform our users about new features in
SGD and to foster communication within the yeast community. You have
received it because you are listed as a contact for SGD in our
database.
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Members of the SGD staff will be present at the 2006 Yeast Genetics and Molecular Biology Meeting at Princeton University from July 25 - 30, 2006. In addition to presenting posters about data and resources available at SGD, we will be soliciting your feedback on how data should be organized. Stop by our demo table and you could win a limited edition SGD T-shirt or cap.
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The SGD full-text literature search (powered by Textpresso) has been expanded, and now includes 44,000+ yeast-related full-text journal articles. The full-text literature search can be accessed via the Full-text search link on the home page, from a link on the SGD Search Options contents page, and from the Literature pulldown menu on the right side of all Locus Summary Pages, where the search form is prefilled with the ORF or gene name.
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New Chromosome History pages have been implemented to view sequence and annotation changes made to the
systematic sequence of S. cerevisiae. These pages display the
complete sequence and annotation history of each chromosome since the
initial release of the systematic
reference sequence on 1996-07-31. Chromosome Histories can be
accessed through the Chromosome
History Search via the Sequencing
Tables link at the bottom left of the home
page under Download Data.
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SGD curators have updated the systematic sequence and its annotation. Sequence and/or annotation changes were made affecting 16 features. Altered or new features are listed in the What's New in SGD for 2006. Details regarding these changes can be found in the
Chromosome
History (see above) of each chromosome and in the "Locus History" pages of affected features.
Files on the SGD
FTP site are updated weekly. The following table lists the
sequence changes made during the last quarter.
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The transcription factor binding sites published by Harbison, et al. (2004) have been remapped to the current S. cerevisiae genome sequence. These data can be viewed in GBrowse and in the "Regulatory Role" section on the Locus Summary Pages (see SUM1). In addition, the regulatory map data from MacIsaac, et al. (2006) are available from the FTP site. Thanks to Kenzie MacIsaac for providing information to remap the binding sites and new data to SGD.
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Gene Summary Paragraphs summarize published biological information for
a gene and its product, and are designed to familiarize both yeast and
non-yeast researchers with the general facts and important subtleties
regarding a locus. During the last quarter, new gene summary
paragraphs for the following 115 genes and chromosomal features have been added to their
respective Locus Summary Pages.
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- SGD has added data to its FTP site (systematic_results directory) from Kastenmayer JP et al. (2006), a study that describes the phenotypes of gene-deletion mutants of 247 small open reading frames (sORFs) in S. cerevisiae. These deletion strains are available as supplemental sets from Open Biosystems.
- The regulatory map data from MacIsaac, et al. (2006) are available from the FTP site. Thanks to Kenzie MacIsaac for providing the new data to SGD.
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- The Gene Ontology Consortium began publishing a newsletter to highlight significant improvements and changes to the ontologies, annotations, and software that are developed by members of the GO Consortium. This newsletter will be sent to those subscribed to the GO Friends mailing list on a quarterly basis. The current newsletter includes a basic tutorial on AmiGO.
- A new resource to search periodic
genes of the yeast Saccharomyces cerevisiae based on a
combined analysis of five cell cycle microarray datasets (Pramila, et
al., in press) has been added to the Expression
Data Resources on the External Links page.
Upcoming Conferences and Courses ( * asterisks indicate attendance by SGD)
- 2006 Yeast
Genetics and Molecular Biology Meeting *
Princeton University, Princeton, NJ
July 25 - July 30, 2006
- Interactome
Networks *
Wellcome Trust Genome Campus, Hinxton, UK
August 30 - September 3, 2006
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24th Small Meeting on Yeast Transport and Energetics
Prague, Czech Republic
August 31 - September 3, 2006
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5th International Meeting on Yeast Apoptosis
Kutna Hora, Czech Republic
September 3 - September 7, 2006
- Yeast
Genome 10th anniversary *
Brussels, Belgium
September 7 - September 8, 2006
- Genome
Informatics *
Wellcome Trust Genome Campus, Hinxton, UK
September 13 - September 17, 2006
- XXIIIrd International
Conference on Yeast Genetics and Molecular Biology *
Melbourne, Australia
July 1 - July 6, 2007
If you think friends or colleagues would be interested in receiving
this newsletter, they can subscribe by filling out a SGD colleague
form selecting 'Y' to become an SGD contact. The form can be found
using this URL:
http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch.
If you are receiving this newsletter by email and do not want to
continue your subscription, you may indicate this by changing the
preference for the question-
Do you want to be a contact for SGD (receive quarterly newsletters)?: from 'Y' to 'N' on your colleague form accessible at:
http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch.
As always, please contact SGD with any comments or suggestions at:
yeast-curator@yeastgenome.org
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