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Search SGD web pages, Global Gene Hunter, Search Literature, and more.
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Getting Started, Sitemap, FAQ, and more.
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BLAST, Gene/Seq Resources, Maps,
and more.
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PDB Homologs, Protein Motifs, Homologs,
and more.
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Protein Info,
Function Junction,
Pathways,
Expression Connection, and more.
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GO Tutorial, What is GO?, GO Slim Mapper,
GO Term Finder, and more.
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Search SGD colleagues, Find yeast labs,
Conferences & Seminars, and more.
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Gene Registry,
Community Annotation,
Colleague update, Contact SGD, and more.
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FTP, Gene Names, Sequencing Tables,
and more.
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Virtual Library, and more.
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Usage statistics, Citing SGD,
Publications, Staff, and more.
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SGDTM is a
scientific database of the molecular biology and genetics of the yeast
Saccharomyces cerevisiae, which is commonly known as baker's or
budding yeast. |
New and Noteworthy |
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SGD Newsletter
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SGD has sent out its quarterly newsletter to colleagues designated as
contacts in SGD. An HTML version of the
newsletter is available. If you would like to receive this letter in
the future please use the Colleague
Submission/Update form to let us know. (Posted November 18, 2004)
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Updates to S288C Sequence
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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 result in annotation changes, such as altering the start 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 gene. Click here for more details on these recent changes, or the Table of Updates to the Systematic Sequence for comprehensive summaries of all changes in the systematic sequence.
(Posted November 17, 2004)
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SGD releases results of the YGM 2004 meeting survey
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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.
(Posted November 17, 2004)
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SGD expands literature search
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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.
(Posted November 16, 2004)
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SGD adds CDE annotations to centromere pages
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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. CDEI, the smallest domain, is an
approximately 8 bp consensus sequence that is bound by centromere
binding factor 1 (Cbf1p). CDEII, the central centromeric domain, is
AT-rich and 75-100 bp in length. CDEIII consists of a 26-bp consensus
sequence that provides the binding site for the centromere DNA binding
factor 3 (CBF3) complex. 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. (Posted October 21, 2004)
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| Literature curation news |
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SGD releases new database architecture
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Over the past six months SGD staff have 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.
(Posted September 2, 2004)
Addendum: 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 this directory:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/
(Posted September 8, 2004)
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SGD Links to the Yeast Protein Localization Database
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The SGD Locus page "Localization Resources" pull-down menu now includes
links to pages at the Yeast Protein Localization database (YPL.db) at
University Graz. The YPL.db contains information about the
localization patterns of yeast proteins. Individual pages at YPL.db
list experimental details and show images of GFP-tagged proteins in live yeast visualized by
Confocal Laser Scanning Microscopy. More information can be found in Habeler et al. (2002) and on
their homepage. Thanks to Sepp Kohlwein and Klaus Natter for setting
up the links.
(Posted August 23, 2004)
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Candida Genome Database is now online
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The Candida Genome Database (CGD) is a new online resource dedicated to collecting genomic information for the human pathogen, Candida albicans. CGD is based on the framework of SGD, and SGD users will easily recognize familiar features. Like SGD, CGD is intended to be a public resource for the fungal research community. It will offer access to genomic sequence data and gene and protein information, as well as such community tools as a colleague search and gene name registry. Still a work in progress, CGD contains over 900 gene product description lines, approximately 1,500 mutant phenotype descriptions and 1,500 Gene Ontology (GO) term assignments, all based on literature curation.
(Posted August 19, 2004)
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Two-hybrid data set added to SGD
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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 Trisha
Davis and Michael Riffle for
providing the data files to SGD.
(Posted August 11, 2004)
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SGD Links to the Ashbya Genome Database
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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.
(Posted August 5, 2004)
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