SGD Newsletter
January 2005
In this issue:
What's New at SGD?
1. References for information on Locus Page
2. New features added to Advanced Search tool
3. Files for computational predictions available
4. SGD's paper in 2005 NAR Database Issue
5. New options for Batch Download Tool
6. New features on Locus Page
7. Expansion of our literature search
8. Information about lab strain backgrounds
Coming Soon: Genome Snapshot
Community News
Relevant URLs
This is the January 2005 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.
If you think friends or colleagues would be interested in receiving
this newsletter, they can subscribe by filling out an SGD colleague
form, found using this url:
http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch
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. References for information on Locus Page
The Locus Page has been updated to display the references that have
been used as citations for the Description, Name Description, and Gene
Product. If references are available, a 'View References' link will be
displayed on top of the locus pages and a citation number will be
listed after the information. These references, along with the
references used in the Summary Paragraph, are listed at the bottom of
the Locus page.
2. New features added to Advanced Search tool
The Advanced Search tool (previously called "Chromosomal Features
Search") provides an easy way to generate lists of genes based on a
variety of criteria. For example, you can retrieve all genes known to
be involved in meiosis, all mitochondrial proteins within a certain
molecular weight, all uncharacterized ORFs, etc. We recently added
new search options to this tool, including interaction and expression
data as well as open reading frame classifications (Dubious, Verified,
Uncharacterized).
3. Files for computational predictions available
Results from two studies ( Troyanskaya et al. (2003) PNAS 100:8348-53
and Lee et al. (2004) Science 306:1555-8) that predict functional
interactions between genes have been added to the SGD ftp site.
4. SGD's paper in 2005 NAR Database Issue
The 2005 Nucleic Acids Research Database issue is now available. This
issue includes a paper by the SGD staff describing the following new
tools at SGD:
- Fungal BLAST (for nucleotide and protein searches against fungal
sequences available at GenBank)
- Model Organism BLASTP Best Hits (for links to curated information
about sequences conserved in other organisms)
5. New options for Batch Download Tool
The Batch Download Tool has been updated so that Gene Ontology (GO)
annotations can be downloaded for a list of standard gene names or
systematic names. The GO annotations can be downloaded simultaneously
with DNA sequences, protein sequences, and chromosomal coordinate
information for the same list of gene games or systematic names. In
addition, links to view "Flanking Features" have been added to the
"Maps & Displays" pull-down menu on the Locus Page and Gene/Sequence
Resources so that neighboring chromosomal features can be viewed and
downloaded.
6. New features on Locus Page
Several new links and features have been added to the Locus Page:
An "Expression Summary" histogram summarizes the number of microarray
experiments (samples) in which the expression changed for that ORF.
This histogram can be found in the lower right hand corner of the
Locus Page under the "Functional Analysis" pull-down menu. It is a
hyperlink to the Expression Connection summary page.
Links to view ATCC/WashU Clones in Gbrowse are available from the
"Maps & Displays" pull-down menu.
Links to GPM DB, a database summarizing mass spec data, are available
from the "Protein Info & Structure" pull-down menu. Thanks to Ron
Beavis for helping set up the links.
7. Expansion of our literature search
In response to comments received in the SGD survey taken at the YGM
meeting this summer, SGD is in the process of expanding its literature
search to add more relevant papers to the database. As a result, you
may notice more references in the Literature Guide of the Locus
Pages. We are in the process of curating these new references and
deleting any that are not relevant. Please feel free to alert us to
any problems that you notice.
8. Information about lab strain backgrounds
SGD has created a Lab Strains 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.
Coming Soon: Genome Snapshot
============================
In response to our users' requests, we are creating a web display to
show an overview of the state of the genome, a Genome Snapshot. This
page will summarize the status of the genome and will be updated in
real time based on the existing data. A graphical view will show the
distribution of ORFs by status: Verified, Uncharacterized, or
Dubious. A table will show the number of each type of feature
(Verified ORFs, tRNA, ARS, etc.) present on each chromosome. Bar
charts will show the distribution of genes annotated to a set of high
level GO terms. We will make an announcement on our home page when the
Genome Snapshot becomes available.
Community News
==============
* 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 12 - May 14, 2005 Seventh International Yeast Lipid Conference,
University of Wales Swansea, UK
* 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
* August 16 - August 21, 2005, Yeast Cell Biology, Cold Spring Harbor
Laboratory, Cold Spring Harbor, NY
* October 26 - October 30, 2005, Genome Informatics, Cold Spring
Harbor Laboratory, Cold Spring Harbor, NY
Relevant URLs
=============
For What's New items:
---------------------
1. Sample url for References for information on Locus Page
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=muc1
2. New features added to Advanced Search tool
http://db.yeastgenome.org/cgi-bin/search/featureSearch
3. Files for computational predictions available
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/systematic_results/published_computational_predictions/
4. SGD's paper in 2005 NAR Database Issue
http://nar.oupjournals.org/cgi/content/full/33/suppl_1/D374?ijkey=81BD5zIUk6RQQ&keytype=ref
5. New options for Batch Download Tool
http://db.yeastgenome.org/cgi-bin/batchDownload
6. Sample url for New features on Locus Page
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=muc1
8. Information about lab strain backgrounds
http://www.yeastgenome.org/straintable.shtml
For Community News items:
-------------------------
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://meetings.cshl.edu/meetings/genome05.shtml
Seventh International Yeast Lipid Conference
http://www.yeastlipidconference.swan.ac.uk/
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
Cold Spring Harbor Yeast Cell Biology
http://meetings.cshl.edu/meetings/yeast05.shtml
Cold Spring Harbor Genome Informatics
http://meetings.cshl.edu/meetings/info05.shtml
