SGD Quarterly Newsletter, Spring 2004

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About this newsletter:

This is the April 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.

As always, please contact SGD with any comments or suggestions at: yeast-curator@genome.stanford.edu

Contents

Sequence updates completed

SGD has recently updated the systematic sequence on several chromosomes. These sequence changes are based on the re-sequencing of portions of the S288C strain background. Some of these sequence changes also result in annotation changes, such as altering the start or stop codons. In addition, we will have corrected the annotations for some genes in cases where the sequence was correct, but the original gene call was not (e.g. new exons/introns, change in the start methionine, etc.)

During the month of February, sequence and/or annotation updates were made on the following chromosomes: III, IV, VI, VIII X, XII, XIII, XIV, and XV. More information about the completed sequence updates can be found at the Table of Updates to the Systematic Sequence.

Large-scale genetic interaction data added

Results from the large-scale genetic interaction study described in Tong et al. (2004) Science 303:808-813 have been incorporated into SGD. These genetic interaction data are displayed on individual SGD locus pages. In addition, you can download all the data from the SGD ftp site, or from the paper's supplemental web site. Thanks to Amy Tong and Charlie Boone for assisting SGD in incorporating their results in order to provide this valuable resource to the yeast community.

Large-scale genetic footprinting data added

Results from a large-scale yeast genetic footprinting study performed by Dunn et al have been incorporated into SGD. Phenotypic profiling of individual genes was achieved by assaying the fitness of multiple independent mutants of each gene during competitive growth under five different conditions. These results are displayed in the Phenotype section of individual SGD locus pages. In addition, you can download all the data from the SGD ftp site. Thanks to Barbara Dunn et al. for releasing these data and providing an abstract to SGD pre-publication.

Expanded annotation of the rDNA region

SGD has expanded its annotation of the S. cerevisiae rDNA locus, RDN1, which consists of 100-200 tandem copies of a 9.1-kb repeat covering approximately 1-2 Mb on the right arm of Chromosome XII. In addition to the three ribosomal RNA coding sequences (for the 18S, 5.8S, and 25S rRNAs), each of the two annotated repeat units (RDN37-1 and RDN37-2) now contains annotated 5' ETS, 3' ETS, ITS1, ITS2, NTS1, and NTS2 spacer regions, including respective locus pages. Thanks to David Tollervey and Christophe Dez for verifying coordinates and providing feedback for these expanded yeast rDNA annotations.

New microarray data sets added

Four data sets have been added to SGD's Expression Connection tool, which allows you to search gene expression data from multiple microarray studies. The data sets that have been added are:

  • Ploidy regulation of gene expression (Galitski et al. (1999) Science 285:251-4)
  • Gene regulation by Swr1, Htz1, and Ino80 (Mizuguchi et al. (2004) Science 303:343-8)
  • Expression regulated by the calcineurin/Crz1 pathway (Yoshimoto et al. J Biol Chem 277:31079-88)
  • Expression during the unfolded protein response (Travers et al. Cell 101:249-58)

These data are also available for download on the SGD ftp site. Thanks to Joe Landry for assisting SGD in loading his data from Mizuguchi et al.

New Fungal BLAST tool

SGD has created a new Fungal BLAST interface that can be used to do BLASTN (nucleotide vs. nucleotide) or TBLASTN (protein vs. translated nucleotide database) searches of any sequence of choice against any combination of fungal sequence datasets, including genome sequences of fungal model organisms and pathogens, ESTs, and other fungal sequence sets in GenBank. The tool is accessible from links on the Analysis & Tools and Homology & Comparisons pages, as well as from the "Comparison Resources" pull-down menu on all SGD Locus pages. Additional fungal sequence datasets will be incorporated as new genomes become available. See SGD's Fungal BLAST help page for more information.

Community News

Ashbya gossypii Genome Database available online The complete sequence and annotation of the A. gossypii genome has been made available at the Ashbya Genome Database (AGD) by Peter Philippsen and colleagues. Results describing how the A. gossypii genome gives insight into the evolution of the S. cerevisiae genome can be read in Dietrich et al. (2004) Science 304:304-7. The genome sequence for A. gossypii is included in the Fungal BLAST tool at SGD.

Upcoming conferences and courses

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

  • 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 at
University of Washington, Seattle, WA. Meeting registration ends
June 28, 2004.
  • August 18 - August 22, 2004: Third International Meeting on Yeast
Apoptosis (IMYA) at Faculty of Natural Sciences of Salzburg
University, Salzburg, Austria


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