SGD Quarterly Newsletter

Posted February 2, 2006

In this issue:

  1. Search for your Favorite Allele and more in 30,000+ Yeast-Related Full Text Articles
  2. Several Sequence and Annotation Changes made to the Systematic Sequence of S. cerevisiae
  3. SGD Publication Describes the Genome Snapshot in the 2006 NAR Database Issue
  4. FTP File Format Changes
  5. Find Related proteins in C. albicans and S. pombe Genomes
  6. Links to Yeast Gene Order Browser Tool Added
  7. 71 New Gene Summary Paragraphs Added
  8. Upcoming Meetings
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About this Newsletter

This is the January 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.

  1. Search for your Favorite Allele and more in 30,000+ Yeast-Related Full Text Articles

    An allele, such as cdc28-1N, can be entered into the search box of SGD's full-text literature search powered by Textpresso. The full text of 30,000+ yeast-related articles will be searched to produce a list of references which mention this allele in the text or in a legend. The full-text literature search can be accessed via the Full-text search on the home page, as a link on the SGD Search Options and from the Literature pull-down menu on the right side of all Locus Summary Pages, where the search form is prefilled with the ORF or gene name.

  2. Several Sequence and Annotation Changes made to the Systematic Sequence of S. cerevisiae

    SGD curators have updated the systematic sequence and its annotation. Sequence and/or annotation changes were made affecting 43 features, and 18 new features have been added. Altered or new features are listed in the What's New in SGD for 2005 and 2006. Details regarding these changes can be found in the Table of Sequence Updates 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.

    List of Sequence/Annotation Changes
    ChromosomeSequence/Annotation ChangesNew Features Added
    ISWH1/YAR042WNone
    II APE3/YBR286W YBR056C-B, YBR201C-A, SNR161/snR161
    III YCL048W-A, AGP1/YCL025C, YCL058W-A None
    IV YDR461C-A, YDR374W-A, YDR119W-A, YDL007C-A, NHP2/YDL208W, LSM6/YDR378C, RRP8/YDR083W None
    V YER030W, RSM18/YER050C SNR80/snR80
    VINoneNone
    VII SPG1/YGR236C, AMA1/YGR225W, YGR226C, CTT1/YGR088W YGL194C-A
    VIII SAE3/YHR079C-A, SOL3/YHR163W, YHL026C None
    IX SEC28/YIL076W, RHR2/YIL053W, CBR1/YIL043C YIL102C-A
    X YJL046W, JJJ2/YJL162C, ASG7/YJL170C None
    XI UTH1/YKR042W, YKL023C-A, YKL065W-A, GLG1/YKR058W, PTM1/YKL039W, UTP11/YKL099C, YKL137W None
    XII YLR146W-A, REC102/YLR329W, DUS3/YLR401C None
    XIIINone snR85, RNA170
    XIV TRF5/YNL299W,YPT11/YNL304W None
    XV CDC21/YOR074C, TMA46/YOR091W, MDM32/YOR147W, MCT1/YOR221C, MIP1/YOR330C, TMA16/YOR252W, FRE7/YOL152W snR81
    XVI JIP5/YPR169W, OAZ1/YPL052W, YPL052W-A YPR145C-A
    MitoAI3/Q0060, AI4/Q0065 None

  3. SGD Publication Describes the Genome Snapshot Resource in the 2006 NAR Database Issue

    The 2006 Nucleic Acids Research Database issue features a paper (HTML | PDF) by the SGD staff describing the new Genome Snapshot resource at SGD.

  4. FTP File Format Changes

    The format of several sequence files on SGD's FTP site has been updated. All updated files are located in:
    ftp://genome-ftp.stanford.edu/pub/yeast/data_download/sequence/genomic_sequence/
    The following changes have been made
    1. Header lines in files found in the orf_dna, orf_protein, rna, and other_features subdirectories have been expanded:
      • old 8-digit SGDIDs replaced with current 10-digit SGDIDs (the same number but with additional padding zeros)
      • a detailed description of the feature, enclosed in quotes, is now included at the end of the header line
    2. The content and header line format of the intergenic/NotFeature.fasta file have been changed:
      • the intergenic sequences and coordinates listed no longer overlap with the flanking genes
      • the header line lists the flanking genes
      • the header format has been changed to be more consistent with those found in other sequence files

  5. Find Related Proteins in C. albicans and S. pombe Genomes

    The Model Organism BLASTP Best Hits resource now includes Candida albicans (CGD) and Schizosaccharomyces pombe (S. pombe GeneDB) in the list of model organisms whose predicted protein sequences have been compared to S. cerevisiae predicted protein sequences. This resource can be accessed from the "Comparison Resources" pull-down menu of the Locus Summary page and also from the Homology & Comparisons page. BLASTP Best Hits results are also available for download from SGD's FTP site.

  6. Links to Yeast Gene Order Browser Added

    The "Comparison Resources" pull-down menu (located on the right hand side of Locus Summary Pages) now includes links to the Yeast Gene Order Browser, a tool used to visualize the syntenic context of protein coding genes from S. cerevisiae, S. castellii, C. glabrata, A. gossypii, K. lactis, K. waltii, and S. kluyveri. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in Byrne and Wolfe.

  7. 71 New Gene Summary Paragraphs

    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 71 genes have been added to their respective Locus Summary Pages.

    List of Gene Summary Paragraphs Added During the Last Quarter
    ADE2/YOR128C ADH1/YOL086C ADH2/YMR303C ADH3/YMR083W ADH4/YGL256W ADH5/YBR145W
    ADR1/YDR216W AVO1/YOL078W AVO2/YMR068W BIT61/YJL058C CDD1/YLR245C FCY1/YPR062W
    FCY2/YER056C FUI1/YBL042C FUR1/YHR128W FUR4/YBR021W GLC7/YER133W GND1/YHR183W
    GND2/YGR256W HO/YDL227C KOG1/YHR186C LSM1/YJL124C LSM2/YBL026W LSM3/YLR438C-A
    LSM4/YER112W LSM5/YER146W LSM6/YDR378C LSM7/YNL147W LSM8/YJR022W LST8/YNL006W
    MAK31/YCR020C-A PSF1/YDR013W PSF2/YJL072C PSF3/YOL146W RBK1/YCR036W RKI1/YOR095C
    RPE1/YJL121C SFA1/YDL168W SLD5/YDR489W SLM1/YIL105C SLM2/YNL047C SMB1/YER029C
    SMD1/YGR074W SMD2/YLR275W SMD3/YLR147C SME1/YOR159C SMX2/YFL017W-A SMX3/YPR182W
    SNX3/YOR357C SOL1/YNR034W SOL2/YCR073W-A SOL3/YHR163W SOL4/YGR248W SPT15/YER148W
    TAL1/YLR354C TCO89/YPL180W TKL1/YPR074C TKL2/YBR117C TSC11/YER093C URA1/YKL216W
    URA10/YMR271C URA2/YJL130C URA3/YEL021W URA4/YLR420W URA5/YML106W URA7/YBL039C
    URA8/YJR103W URH1/YDR400W URK1/YNR012W ZWF1/YNL241C YJL068C

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

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