SGD Quarterly Newsletter

Posted May 7, 2007

In this issue:

  1. Community Wiki available
  2. SNPs Between Reference Strain S288C and Seven Common Lab Strains
  3. New Summary Paragraphs Added
  4. GO Annotations from GOA-UniProt Added
  5. 5' UTR Introns Added
  6. Sequence and Annotation Changes Made to the Systematic Sequence of S. cerevisiae
  7. Upcoming Meetings
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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 have received it because you are listed as a contact for SGD in our database.

  1. 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.

  2. 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.

  3. New 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/YLR002W SNM1/YDR478W SOD1/YJR104C STE11/YLR362W
    STE20/YHL007C 85 RPL* genes56 RPS* genes7 RPP* genes 50 Retrotransposons
    382 Long Terminal Repeats 89 Transposable Element Genes

  4. 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. 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.

  6. 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.

    ChromosomeSequence/Annotation ChangesNew Features Added
    I HRA1, YAL004W, SSA1/YAL005CARS102, ARS103, ARS105, ARS108, ARS109, ARS111, ARS112
    II YBLCtau1, YBRCtau2, YBLCdelta7, YBRCdelta11, YBRCdelta14, YBRCdelta19None
    IIIARS317, YCLCdelta1, YCRCdelta14, YCRCdelta6, YCRCdelta7 None
    IVsnR47, YDRCsigma4, YDRWsigma2, ARS416, ARS404ARS400
    VYERCdelta8None
    VIYFR045W, ARS601, ARS602, ARS604, ARS605, ARS606, ARS607, ARS608, ARS609, ARS603.5, ARS603ARS610
    VIINoneNone
    VIIINoneNone
    IXYILWdelta2None
    XYJRCdelta19, YJRCdelta16, YJRCdelta15None
    XINoneNone
    XIIYLRWdelta24 ARS1200*
    XIIINoneNone
    XIVNoneNone
    XVYRF1-8/YOR396WNone
    XVINoneNone

  7. Upcoming Conferences and Courses (*asterisks indicate attendance by SGD)

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CONTACT SGD: yeast-curator@yeastgenome.org
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