SGD Quarterly Newsletter, Spring 2007

About this newsletter:

This is the May 2007 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 can also subscribe to SGD's RSS feed to receive updates on SGD news - http://www.yeastgenome.org/feed

Details of these items can be viewed at the SGD Blog

Community Wiki Available

In order to facilitate sharing of information about S. cerevisiae genes, gene products, and resources within the yeast community, SGD now includes a Community Wiki. Like the popular Wikipedia, the SGD Community Wiki is a set of web pages that allow users to easily add and edit information. This Community Wiki has been pre-loaded with basic locus information from SGD as well as user annotations previously submitted through the Community Annotation pages. We invite the research community to further develop and enhance the information on the wiki pages. For example, the Wiki would be the ideal place to share comments on particular deletion strains or record differences in mutant phenotypes in different strain backgrounds. Links are available in the "Additional Information" section and from the "Literature" pull-down of each Locus Summary page as well as on the Community Info contents page.

Nucleotide-level Variation Among Commonly Used Yeast Strains

Schacherer et al. identify SNPs between S288c and seven commonly used lab strains; these data are available on the SGD FTP site and can be searched and viewed online via the Yeast SNPs Browser available at Princeton University.

New or Updated Summary Paragraphs

Summary Paragraphs summarize published biological information for a gene/feature, 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 (February - April 2007), new summary paragraphs for the following 695 features have been added to their respective Locus Summary pages.

List of Summary Paragraphs Added During the Last Quarter

ADE12/YNL220W	ADE13/YLR359W	AGX1/YFL030W	CDC53/YDL132W	DNF1/YER166W
DNF2/YDR093W	DNF3/YMR162C	DRS2/YAL026C	ERS1/YCR075C	FAB1/YFR019W
IRA1/YBR140C	IRA2/YOL081W	MIG1/YGL035C	MLC1/YGL106W	MLC2/YPR188C
MLH1/YMR167W	NEO1/YIL048W	NME1	PCA1/YBR295W	RMP1/YLR145W
RTT109/YLL002W	SDO1/YR002W	SNM1/YDR478W	SOD1/YJR104C	STE11/YLR362W
STE20/YHL007C	85 RPL genes	56 RPS genes	7 RPP genes	50 Retrotransposons
382 Long Terminal Repeats	89 Transposable Element Genes

GO Annotations from GOA-UniProt Added

SGD has incorporated manual GO annotations for S. cerevisiae proteins from the GO Annotation (GOA) project at EBI. These annotations can be identified at SGD by the source, e.g., 'UniProt', displayed on the 'Assigned By' column of the GO evidence and references page. The GO evidence and references page can be accessed by clicking on the 'Gene Ontology' tab from any Locus Summary page (e.g., please see Gene Ontology evidence and references page for RSC6). The gene_associations.sgd file, which provides a complete set of manual GO annotations for S. cerevisiae, now includes these annotations from the GOA UniProt file.

5' UTR introns Added

Locus Summary page annotation has now been expanded to include introns located in the 5'-untranslated regions (5' UTRs) of primary transcripts. The Advanced Search can be used to obtain a complete list of genes with 5' UTR introns. We thank the many researchers who generated these data and reviewed our incorporation of it, including Manny Ares, Paul Cliften, Zhihong Zhang, Kara Juneau, and Takashi Ito.

Sequence and Annotation Updates

As new data become available, SGD curators update the systematic sequence and its annotation. Information regarding sequence and annotation changes can be found via the Summary of Chromosome Sequence and Annotation Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly. During the last quarter (February - April 2007), sequence and annotation changes were made affecting 37 features and 11 new features were added.

Chromosome	Sequence/Annotation Changes	New Features Added
I	HRA1, YAL004W, SSA1/YAL005C	ARS102, ARS103, ARS105, ARS108, ARS109, ARS111, ARS112
II	YBLCtau1, YBRCtau2, YBLCdelta7, YBRCdelta11, YBRCdelta14, YBRCdelta19	None
III	ARS317, YCLCdelta1, YCRCdelta14, YCRCdelta6, YCRCdelta7	None
IV	snR47, YDRCsigma4, YDRWsigma2, ARS416, ARS404	ARS400
V	YERCdelta8	None
VI	YFR045W, ARS601, ARS602, ARS604, ARS605,ARS606, ARS607, ARS608, ARS609, ARS603.5, ARS603	ARS610
VII	None	None
VIII	None	None
IX	YILWdelta2	None
X	YJRCdelta19, YJRCdelta16, YJRCdelta15	Example
XI	None	None
XII	YLRWdelta24	ARS1200
XIII	None	None
XIV	None	None
XV	YRF1-8/YOR396W	None
XVI	None	None

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

• The Biology of Genomes*

Cold Spring Harbor Laboratory, New York

May 8 - 12, 2007

• Fourth International Fission Yeast Meeting*

Copenhagen, Denmark

June 11 - 16, 2007

• Conference on Physiology of Yeasts and Filamentous Fungi (PYFF3)

Helsinki, Finland

June 13 - 16, 2007

• XXIIIrd International Conference on Yeast Genetics and Molecular Biology*

Melbourne, Australia

July 1 - 6, 2007

• Yeast Cell Biology*

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

August 15 - 19, 2007

Abstract Deadline: May 23, 2007

• ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution

Hotel Eden Roc, Sant Feliu de Guixols (Costa Brava), Spain

October 20 - 25, 2007

Abstract Deadline: August 1, 2007

• Genome Informatics*

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

November 1 - 5, 2007

Abstract Deadline: August 1, 2007

asterisks indicate attendance by SGD.*

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