SGD Quarterly Newsletter, Fall 2004

About this newsletter:

This is the November 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 is collecting Strain Background Information

SGD has created a Strain Background Summary page describing strains commonly used by yeast researchers, such as S288C, SK1, Sigma 1278B and W303. We will continue to add information on genotypes and important phenotypes for these backgrounds and others. If you have information that should be included, please send an e-mail with the information and a reference, if possible, to yeast-curator@genome.stanford.edu. Thank you!

Results of SGD survey given at YGM 2004

At the recent Seattle Yeast Genetics & Molecular Biology Meeting (YGM), SGD curators circulated copies of a user survey to all meeting attendees. The purpose of the survey was to collect feedback from our users regarding the current features and tools that SGD provides, as well as to gather ideas about new information and tools that our users would like to see in the future. The results of the 2004 SGD survey are now available at the URL below.

Updates to S288C sequence

Updating the reference sequence is an ongoing project at SGD. All sequence updates are based on the re-sequencing of portions of the S288C strain background, and many also result in annotation changes, such as altering the start and/or stop codons. In the past 6 months, the sequence of 16 ORFs has been updated, 3 new ORFs have been added, and one ORF has been merged with a neighboring ORF. See the "What's New In SGD" page for more details on these recent changes, or the Table of Updates to the Systematic Sequence for summaries of all changes to the systematic sequence.

Sequence Annotations are added for CEN1-CEN16

The CEN1-CEN16 centromere pages have been expanded to include sequence annotations for CDEI, CDEII, and CDEIII, the three adjacent DNA elements that comprise each yeast centromere. These expanded pages also contain a new summary paragraph and figure describing the function of the centromere and proteins that bind to CDEI, II, and III. SGD thanks Dr. Sue Biggins for advice about this project.

SGD releases new Database Architecture

SGD staff has worked to significantly enhance the way data are stored at SGD. During this time, much of the data has been checked and updated as needed. These changes will allow SGD to incorporate new data and datatypes, such as additional chromosomal features, with greater ease. As part of this release, several new options have been added to existing tools and there have been some changes and additions to data provided at SGD. We have made every attempt to thoroughly test the performance of the new database but please do not hesitate to contact SGD if you notice any problems with any of our pages.

Files on FTP site have changed

To reflect changes in the database, several files on the ftp site have changed. The SGD_features.tab file replaces the chromosomal_feature.tab and intron_exon.tab files. The dbxref.tab file replaces the external_id.tab file. More information can be found in the README located in the chromosomal_feature directory on the ftp site.

SGD Links to the Yeast Protein Localization Database

SGD announces links to Yeast Protein Localization Database (YPL.db) at University Graz from the "Localization Resources" pull-down menu on Locus pages. Thanks to Sepp Kohlwein and Klaus Natter for setting up the links.

Candida Genome Database is now online

SGD announces that the Candida Genome Database (CGD) is now live. The CGD is based on the framework of SGD.

Two-hybrid data set added to SGD

The two-hybrid results described in Hazbun et al. (2003) Mol Cell 12:1353-1365, have been added to SGD and are now shown on individual locus pages, under the Physical Interactions section. Thanks to Michael Riffle for providing the data files to SGD.

SGD Links to the Ashbya Genome Database

The SGD Locus page "Comparison Resources" pull-down menu now includes links between S. cerevisiae genes and Ashbya gossypii homologs at the Ashbya Genome Database (AGD). These homology determinations were based on analyses performed by Dietrich, et al and Brachat, et al. In addition, Ashbya gossypii predicted protein sequences have been added to SGD's "Model Organism BLASTP Best Hits" resource. Links to this resource can also be found on each Locus Page under the "Comparison Resources" pull-down menu. Thanks to Michael Primig and Leandro Hermida for setting up the links.

Community News

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

• March 12 - March 18, 2005 FEBS Advanced Lecture Course on Systems Biology: From Molecules and Modelling to Cells, Gosau, Austria

• March 15 - March 20, 2005 Twenty Third Fungal Genetics Conference, Asilomar Conference Center, Pacific Grove, CA

• May 11 - May 15, 2005 The Biology of Genomes, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

• May 21 - May 28, 2005 FEBS Advanced Lecture Course on Human Fungal Pathogens: Molecular Mechanisms of Host-Pathogen Interactions and Virulence, La Colle sur Loup, France

• August 7 - August 12, 2005 XXII International Conference on Yeast Genetics and Molecular Biology INCHEBA Exhibition & Fair Center, Bratislava, Slovak Republic

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