SGD Newsletter
January 2004
In this issue:
What's New at SGD?
1) Links to Yeast Resource Center
2) New GO Slim of macromolecular complex terms
3) Sequence updates
4) SGD article in NAR Database issue
5) Thank You to SGD Advisory Board
Community News
Relevant URLs
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. You have received it because you are listed as a contact for SGD in our database. Information on how to unsubscribe is at the bottom of this newsletter.
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
What's New at SGD?
==================
1) 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.
2) 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.
3) 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
4) 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)
5) 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. Abstract submission will open in early March.
URLs mentioned in this Newsletter
=========================
Yeast Resource Center
http://www.yeastrc.org/unknown_orfs/
go_protein_complex_slim.tab
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/
GO Tutorial
http://www.yeastgenome.org/help/gotutorial.html
GO Consortium home page
http://www.geneontology.org/index.shtml
Chromosomal Sequence Updates
http://www.yeastgenome.org/sequenceupdates.shtml
Annotation changes
http://www.yeastgenome.org/chromosomeupdates/annotation_changes.html
Nucleic Acids Research database issue
http://nar.oupjournals.org/content/vol32/suppl_1/
Fungal Alignment Viewer
http://db.yeastgenome.org/cgi-bin/FUNGI/nph-showAlign
Sequence Similarity Query
http://db.yeastgenome.org/cgi-bin/homolog/nrHomolog
Yeast Biochemical Pathways
http://pathway.yeastgenome.org/biocyc/
Find Chromosomal Features
http://db.yeastgenome.org/cgi-bin/search/featureSearch
URLs for conferences/courses
=========================
1) Physiology of Yeasts and Filamentous Fungi:
http://pyff2.insa-tlse.fr/
2) Gene Transcription in Yeast: EuroConference:
http://www.esf.org/esf_euresco_conference.php?language=0&conference=103&meeting=5&page=1
3) Yeast Chromosome Structure, Replication and Segregation:
http://src.faseb.org/2004_sch.htm
4) 2004 Yeast Genetics & Molecular Biology:
http://genetics.faseb.org/genetics/g-gsa/future_meetings.shtml
