SGD Newsletter 2004-11-18

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SGD Newsletter 2004-11-18

SGD Newsletter
November 2004

In this issue:

What's new at SGD?

1) SGD is collecting Strain Background Information
2) Results of SGD survey given at YGM 2004
3) Updates to S288C sequence
4) Sequence annotations are added for CEN1-CEN16
5) SGD releases new database architecture
6) Files on FTP site have changed
7) SGD links to the Yeast Protein Localization Database
8) Candida Genome Database is now online
9) Two-hybrid data set added to SGD
10) SGD links to the Ashbya Genome Database

Community news
Relevant URLs

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. 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) 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!

2) 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.

3) 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.

4) 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.

5) 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.

6) 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.

7) 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.

8) 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.

9) 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.

10) 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

* 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

URLs mentioned in this newsletter
=================================

1) Strain Background Summary Page
http://www.yeastgenome.org/straintable.shtml

2) Results of SGD survey at YGM meeting
http://yeastgenome.org/surveys/YGM04.html

3) Details of S288C Sequence Updates
http://www.yeastgenome.org/whats_new.shtml
http://www.yeastgenome.org/sequenceupdates.shtml

4) Example URL for CEN pages
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=CEN1

5) Enhancements to SGD
http://www.yeastgenome.org/whats_new.shtml#sgd_enhancements

6) README document for chromosomal_feature files on FTP site
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/

7) Yeast Protein Localization Database
http://ypl.uni-graz.at/pages/home.html

8) Candida Genome Database
http://www.candidagenome.org/

9) Hazbun et al. paper with 2-hybrid data
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14690591&dopt=Abstract

10) Ashbya Genome Database
http://agd.unibas.ch/

10) A. gossypii - S. cerevisiae comparisons by Dietrich et al. and Brachat et al.
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=42630
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=37849

FEBS Lecture Course on Systems Biology
http://www.febssysbio.net/

Asilomar Fungal Genetics Conference
http://www.genetics-gsa.org/genetics/fungal-conf/

Cold Spring Harbor Biology of Genomes
http://meet1.cshl.edu/meetings/genome05.shtml

FEBS Lecture Course on Human Fungal Pathogens
http://www.pasteur.fr/infosci/conf/hfp2005/Introduction.html

International Conference on Yeast Genetics and Molecular Biology in Bratislava
http://yeast2005.org