SGD Quarterly Newsletter, Summer 2004

About this newsletter:

This is the July 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

SGD curators at YGM

SGD curators will be attending the 2004 Yeast Genetics and Molecular Biology Meeting in Seattle next week (July 27 - August 1). We will have a demonstration table and are presenting four posters (172A, 502A, 509B, 541A) on tools and resources at SGD. Stop by to ask questions or get an individual tutorial. Fill out a user survey, and receive a super SGD bottle opener!

New BLASTP Best Hits resource available

SGD has a new resource, "Model Organism BLASTP Best Hits", that displays the results of NCBI BLASTP analysis using the protein sequence of each S. cerevisiae open reading frame as the query against the predicted protein sequences of several model organisms. Results are linked to the web pages of the hit proteins in other model organism databases. Currently, the species queried are: human, fruit fly, worm, Arabidopsis, and S. cerevisiae; we expect to add more species in the future. A link to the Best Hits display is found in the 'Comparison Resources' pull-down menu on the right-hand side of the SGD Locus page of each protein-coding gene.

New microarray data set added

A new data set has been added to SGD's Expression Connection tool, which allows you to search gene expression data from multiple microarray studies. The data set added is entitled "Gene regulation by SWR1, HTZ1, and SIR2" (Meneghini et al. (2003) Cell 112:725-36 and Kobor et al. (2004) PLoS Biol 2:E131). The associated data are also available for download on the SGD ftp site. Thanks to Hiten Madhani for assisting SGD in loading his data from Meneghini et al. and Kobor et al.

New links added to SGD Locus pages

The following new links to databases describing different phenotypes of deletion strains have been added under the Functional Analysis pull-down menu on the locus page:

PROPHECY: provides quantitative information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains

SCMD: a collection of micrographs of budding yeast mutants

Thanks to Luciano Fernandez-Ricaud for setting up the links to PROPHECY and Shinichi Morishita and Yoshikazu Ohya for setting up the links to SCMD.

GFF3 file released

SGD has released a GFF3 file for the S. cerevisiae genome that provides genomic features, gene names and aliases, gene descriptions, GO annotations, and more. This file meets the current GFF3 specifications and is fully compatible with GBrowse and Chado loading scripts. Thanks to Scott Cain of the Generic Model Organism Database project (GMOD) for assistance during testing. The GFF3 file is updated once a week from the SGD database and is available for download from the SGD FTP site.

First release of SGD Lite

SGD announces the release of SGD Lite, a lightweight version of SGD in a freely available database system, which can be easily downloaded and installed on a personal desktop for your own research or development purposes. SGD Lite has been implemented in its entirety by using the components provided by the Generic Model Organism Database Construction Set as part of the GMOD project.

New Batch Download tool available

SGD announces the release of a Batch Download Tool that allows simultaneous retrieval of DNA sequences, protein sequences, and chromosomal coordinates for a list of Standard Gene Names or Feature Names. This tool can be accessed through links on the Analysis & Tools and Download Data contents pages.

SGD proposes new FTP file

SGD is planning on adding additional types of chromosomal features (such as promoters, regulatory regions, and UTR introns) to the database. In order to provide the data to the scientific community in a convenient format, SGD is proposing a new FTP file which would replace the current chromosomal_feature.tab and intron_exon.tab files. A proposal describing the format of this new file is available at SGD (linked from the announcement on the home page; also see below for the URL). If you have used either the chromosomal_feature.tab or intron_exon.tab file in the past, SGD would appreciate your input regarding whether this new FTP file will provide the same type of information for you. Please send comments to yeast-curator@genome.stanford.edu.

GBrowse available

GBrowse, an interactive genome browser that can be customized to show selected chromosomal features as well as display user provided annotations, has been implemented at SGD. It is currently available from the Analysis & Tools contents page and from the BLAST results pages. GBrowse was developed by the Generic Model Organism Database (GMOD) project. Thanks to Scott Cain of GMOD for assistance during testing.

Community News

Upcoming conferences

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

• July 27 - August 1, 2004: 2004 Yeast Genetics & Molecular Biology at

University of Washington, Seattle, WA.

• 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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