SGD Quarterly Newsletter, Winter 2004

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About this newsletter:

This is the January 2004 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.

Other relevant URLs mentioned in this newsletter are also at the bottom of the page. As always, please contact SGD with any comments or suggestions at: yeast-curator@genome.stanford.edu

Contents

Links to Yeast Resource Center added

Based on the analysis published by Hazbun et al. (Hazbun, T. R., et al. (2003) Mol Cell 12:1353-1365), SGD curators have updated GO annotations for 61 uncharacterized but essential ORFs. In addition, links to the Yeast Resource Center Informatics Platform have been added to the localization, interaction, and/or protein info pull-down menus as appropriate for each ORF. Thanks to Michael Riffle and Trisha Davis for setting up the links.

New GO Slim of Macromolecular Complex Terms

SGD has created a new GO Slim, consisting of a set of macromolecular complex terms. A GO-Slim is a selection of high-level terms from the Biological Process, Molecular Function, or Cellular Component ontology that represents major branches of that ontology. To create this GO Slim set, we chose very granular protein complex terms from the cellular component ontology that would be likely to indicate a functional relationship among gene products that are annotated to a particular term. For example, gene products that are co-localized to the ribosome are likely to share a role in protein biosynthesis. A file (go_protein_complex_slim.tab) that contains gene products mapped to these terms can be found on our ftp site. For more information on GO Slim sets and the GO project in general, see the GO tutorial at SGD and the GO Consortium web page.

Sequence Updates In Progress

The systematic sequence is being updated by SGD, based on the re-sequencing of portions of the S288C strain background. Some of these updates result in annotation changes, such as altering start or stop codons. At the same time, we are also updating additional annotation changes that resulted from experimental evidence other than sequence errors. More information about these sequence updates can be found at the Table of Updates to the Systematic Sequence:

http://www.yeastgenome.org/sequenceupdates.shtml

http://www.yeastgenome.org/chromosomeupdates/annotation_changes.html

SGD article in NAR Database issue

The 2004 Nucleic Acids Research Database Issue is now available. This issue contains a paper (Christie, K. R., et al. (2004) Nucleic Acids Research 32:D311-D314) by the SGD staff describing four new tools in SGD:

  • Fungal Alignment Viewer (for a ClustalW alignment of related fungal sequences)
  • Sequence Similarity Query tool (for results of a PSI-BLAST query to find related sequences from any organism)
  • Yeast Biochemical Pathways tool (for information about metabolic pathways in S. cerevisiae)
  • Find Chromosomal Features search interface (for an advanced search based on criteria like molecular weight or pI)

Thank You to the SGD Advisory Board

The SGD staff wishes to thank the members of its advisory board for a very productive advisory meeting in early November. The board, composed of experts on model organism databases, comparative genomics, bioinformatics, yeast genomics, and yeast cell biology, spent a day and a half at SGD discussing ways in which we can continue to meet the needs of the yeast community. Many thanks to them for their help!

Community News

Upcoming Conferences and Courses

  • March 24-28, 2004: Physiology of Yeasts and Filamentous Fungi at Anglet, France.
  • May 29 - June 3, 2004: Gene Transcription in Yeast: EuroConference, at San Feliu de Guixols, Spain.
  • July 10-15, 2004: Yeast Chromosome Structure, Replication and Segregation at Callaway Gardens, Pine Mountain, GA.
  • July 27 - August 1, 2004: 2004 Yeast Genetics & Molecular Biology, University of Washington, Seattle, WA.


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