SGD Quarterly Newsletter, Summer 2006

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About this newsletter:

This is the July 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.

Visit SGD at the Yeast Genetics and Molecular Biology Meeting - Win a T-shirt or Cap

Members of the SGD staff will be present at the 2006 Yeast Genetics and Molecular Biology Meeting at Princeton University from July 25 - 30, 2006. In addition to presenting posters about data and resources available at SGD, we will be soliciting your feedback on how data should be organized. Stop by our demo table and you could win a limited edition SGD T-shirt or cap.

Search for a Strain Background and more in 44,000+ Yeast-Related Full Text Articles

The SGD full-text literature search (powered by Textpresso) has been expanded, and now includes 44,000+ yeast-related full-text journal articles. The full-text literature search can be accessed via the Full-text search link on the home page, from a link on the SGD Search Options contents page, and from the Literature pulldown menu on the right side of all Locus Summary Pages, where the search form is prefilled with the ORF or gene name.

View Updates to the Systematic Sequence on New Chromosome History Pages

New Chromosome History pages have been implemented to view sequence and annotation changes made to the systematic sequence of S. cerevisiae. These pages display the complete sequence and annotation history of each chromosome since the initial release of the systematic reference sequence on 1996-07-31. Chromosome Histories can be accessed through the Chromosome History Search via the Sequencing Tables link at the bottom left of the home page under Download Data.

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 16 features. Altered or new features are listed in the What's New in SGD for 2006. Details regarding these changes can be found in the Chromosome History (see above) of each chromosome 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
Chromosome Sequence/Annotation Changes New Features Added
I CEN1 None
II None None
III None None
IV CEN4 None
V UTR4/YEL038W, CEN5 None
VI CEN6 None
VIII None None
IX CEN9 None
X YJR003C None
XI EMC3/YKL207W, KKQ8/YKL168C, CAF4/YKR036C None
XII None None
XIV ZIM17/YNL310C, SPS19/YNL202W None
XV MCA1/YOR197W None
XVI CEN16 None
Mito None None

Transcription Factor Data Remapped to Updated Sequence

The transcription factor binding sites published by Harbison et al. (2004) have been remapped to the current S. cerevisiae genome sequence. These data can be viewed in GBrowse and in the "Regulatory Role" section on the Locus Summary Pages (see SUM1). In addition, the regulatory map data from Maclsaac et al. (2006) are available from the FTP site. Thanks to Kenzie MacIsaac for providing information to remap the binding sites and new data to SGD.

New Summary Paragraphs for 115 Genes and Chromosomal Features

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 115 genes and chromosomal features have been added to their respective Locus Summary Pages.

List of Summary Paragraphs Added During the Last Quarter
RAD54/YGL163C SPT8/YLR055C STE50/YCL032W YRF1-1/YDR545W YRF1-2/YER190W YRF1-3/YGR296W
YRF1-4/YLR466W YRF1-5/YLR467W YRF1-6/YNL339C YRF1-7/YPL283C ARS101/ARS109 ARS1020
ARS1021 ARS1022 ARS1023 ARS1024 ARS1025 ARS110
ARS1208 ARS1411 ARS1412 ARS1413 ARS1414 ARS1501
ARS1502 ARS1516 ARS209 ARS300 ARS301 ARS302
ARS303 ARS304 ARS305 ARS306 ARS307 ARS308
ARS309 ARS310 ARS313 ARS314 ARS315 ARS316
ARS317 ARS318 ARS319 ARS320 ARS404 ARS1/ARS416
ARS422 ARS502 ARS503 ARS504 ARS507 ARS508
ARS510 ARS511 ARS512 ARS513 ARS514 ARS515
ARS516 ARS517 ARS518 ARS519 ARS520 ARS521
ARS522 ARS523 ARS600 ARS601 ARS602 ARS603
ARS603.5 ARS604 ARS605 ARS606 ARS607 ARS608
ARS609 ARS701 ARS706 ARS805 ARS2/ARS808 ARS901/ARS913
ARS1001 ARS1002 ARS1003 ARS1004 ARS1005 ARS1006
ARS1007 ARS1008 ARS1009 ARS1010 ARS1011 ARS1012
ARS1013 ARS1014 ARS1015 ARS1016 ARS1017 ARS1018

New Datasets Added

  1. SGD has added data to its FTP site (systematic_results directory) from Kastenmayer JP et al. (2006), a study that describes the phenotypes of gene-deletion mutants of 247 small open reading frames (sORFs) in S. cerevisiae. These deletion strains are available as supplemental sets from Open Biosystems.
  2. The regulatory map data from MacIsaac, et al. (2006) are available from the FTP site. Thanks to Kenzie MacIsaac for providing the new data to SGD.

Community News

  • The Gene Ontology Consortium began publishing a newsletter to highlight significant improvements and changes to the ontologies, annotations, and software that are developed by members of the GO Consortium. This newsletter will be sent to those subscribed to the GO Friends mailing list on a quarterly basis. The current newsletter includes a basic tutorial on AmiGO.
  • A new resource to search periodic genes of the yeast Saccharomyces cerevisiae based on a combined analysis of five cell cycle microarray datasets (Pramila, et al., in press) has been added to the Expression Data Resources on the External Links page.

Upcoming Conferences and Courses

Information on registration and abstract deadlines for the following conferences is available at:

  • 2006 Yeast Genetics and Molecular Biology Meeting *
Princeton University, Princeton, NJ
July 25 - July 30, 2006
  • Interactome Networks *
Wellcome Trust Genome Campus, Hinxton, UK
August 30 - September 3, 2006
  • 24th Small Meeting on Yeast Transport and Energetics
Prague, Czech Republic
August 31 - September 3, 2006
  • 5th International Meeting on Yeast Apoptosis
Kutna Hora, Czech Republic
September 3 - September 7, 2006
  • Yeast Genome 10th anniversary *
Brussels, Belgium
September 7 - September 8, 2006
  • Genome Informatics *
Wellcome Trust Genome Campus, Hinxton, UK
September 13 - September 17, 2006
  • XXIIIrd International Conference on Yeast Genetics and Molecular Biology *
Melbourne, Australia
July 1 - July 6, 2007

asterisks indicate attendance by SGD.*

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