SGD Newsletter
July 2004
In this issue:
What's new at SGD?
1) SGD curators at YGM
2) New BLASTP Best Hits resource available
3) New microarray data set added
4) New links added to SGD Locus pages
5) GFF3 file released
6) First release of SGD Lite
7) New Batch Download tool available
8) SGD proposes new FTP file
9) GBrowse available
Community news
Relevant URLs
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. 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 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!
2) 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.
3) 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.
4) 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.
5) 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.
6) 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.
7) 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.
8) 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.
9) 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
* 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
URLs mentioned in this newsletter
=================================
SGD home page:
http://www.yeastgenome.org/
SGD ftp site:
ftp://genome-ftp.stanford.edu/pub/yeast/
Expression Connection:
http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl
Meneghini et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=37108
Kobor et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=42634
Download microarray data from SGD ftp site:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/systematic_results/
expression_data/
PROPHECY database:
http://prophecy.lundberg.gu.se/
Saccharomyces cerevisiae Morphological Database (SCMD):
http://yeast.gi.k.u-tokyo.ac.jp/
Download GFF3 file from SGD:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/
saccharomyces_cerevisiae.gff
Generic Model Organism Database home page:
http://www.gmod.org/
Download SGD Lite:
http://sgdlite.princeton.edu/
Batch Download Tool:
http://db.yeastgenome.org/cgi-bin/batchDownload
Analysis & Tools page:
http://www.yeastgenome.org/ATContents.shtml
Download Data page:
http://www.yeastgenome.org/DownloadContents.shtml
Description of Proposed New FTP File Format:
http://www.yeastgenome.org/help/newFTPproposal.html
GBrowse:
http://www.yeastgenome.org/cgi-bin/gbrowse/yeast
2004 Yeast Genetics & Molecular Biology Meeting
http://www.yeast-meet.org/
Third International Meeting on Yeast Apoptosis (IMYA)
http://www.yeast-apoptosis.org/html/
