External Links
Contents
General Yeast Resources
describes the yeast model organisms: Saccharomyces cerevisiae (budding, bakers', and sometimes brewers'), Schizosaccharomyces pombe (fission), and Candida albicans. Includes information for non-specialists and teachers.
search the Yeast Biosci Newsgroup
Nucleic Acid Data Resources
sequence repository at the NCBI, Bethesda, Maryland, USA
sequence repository at the EBI, Hinxton Hall, Cambridge, UK
sequence repository at Mishima, Japan
software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences
catalog of confirmed and predicted DNA replication origin sites, currently limited to S. cerevisiae
explore promoter regions by searching for genes or a sequence. Also contains a list of yeast transcription factor binding sites.
search for regulatory signals in the non-coding sequences of S. cerevisiae, S. pombe, and other organisms
explore the promoter regions of all ORFs in the yeast genome. Note that this web site is not exhaustive, and some of the information is outdated.
search tool for identification and analysis of conserved patterns in Saccharomyces promoters. Formore information, please refer to Kohli DK, et al (2004) In Silico Biol 4(3):0034]
yeast intron data from the Ares Lab, U.C. Santa Cruz
yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts
yeast tRNA information from Todd Lowe, UC-Santa Cruz
Genome and Protein Resources
A collection of papers describing the sequencing of each chromosome of the S. cerevisiae genome
This website provides structural assignments to protein sequences at the
superfamily level. You can browse an overview of all the superfamilies currently identified in S. cerevisiae; the site
also provides several different ways to search this
information. See Gough et al. for more information.
- Genome Sequence Center: BLAST Serverat the Washington University GSC in St. Louis. BLAST searches may be performed against genomic sequences from five Saccharomyces species: S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri.
yeast information from the Munich Information Center for Protein Sequences (MIPS)
yeast protein information from Incyte Genomics, Inc. Access to this resource requires a subscription.
Links between functionally related yeast proteins are used to predict functions for about two thirds of all predicted yeast proteins in Marcotte et al. (1999) Nature 402:83-86.
Yeast transposon tagging data from the Yale Genome Analysis Center.
The Fields lab's systematic Two-Hybrid project. Results are described in Uetz et al. (2000) Nature 403:623-627.
a database of genetic and physical interactions.
BioGRID, developed in Mike Tyers group, contains
interaction data from many sources, including both small-scale and
genome/proteome-wide studies, the MIPS
database, and BIND.
a powerful application for graphically representing physical and genetic biological interactions. It
provides many features that are helpful in analysis of interaction data. Osprey is also coupled with the General Repository of Interaction Datasets (BioGRID) and as a result brings a large dataset of interactions to your fingertips.
provides protein searching from multiple yeast databases and provides
experimental data from mass spectrometry, yeast two-hybrid,
fluorescence microscopy, protein structure prediction and
protein complex predictions for S. cerevisiae
proteins. Please see Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82 for more information.
a database of mass spectrometry based proteomics information, populated by the general proteomics community.
a tool used to visualize the syntenic context of any gene from
S. cerevisiae, S. castellii, C. glabrata,
A. gossypii, K. lactis, K. waltii, and
S. kluyveri. This tool was developed by Kevin Byrne and Ken
Wolfe (Trinity College, Dublin, Ireland), as described in Byrne and Wolfe.
a tool to view orthologous proteins from eukaryotic orgranisms
(Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana,
Drosophila melanogaster, Caenorhabditis elegans, Plasmodium
falciparum, Schizosaccharomyces pombe, and Saccharomyces
cerevisiae). This tool provides information from KOGs, Inparanoid,
Homologene, OrthoMCL and manually curated orthologs between S. cerevisiae and S. pombe. This tool was developed by Penkett CJ, Morris JA, Wood V, and Bahler J (Wellcome Trust Sanger Institute, Cambridge, UK).
an iPhone application containing proteome information for several
different Saccharomyces and Schizosaccharomyces strains
a compiled and systematic reference map of nucleosome positions across the S. cerevisiae genome
Expression Data Resources
A curated database of regulatory associations
between transcription factors and their target genes, and
information on transcription factor binding sites (see Monteiro et al.</a, (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).
A website for visualizing and studying periodic
transcription in yeast (see Kudlicki et al. (2007) Bioinformatics)
Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies href="/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman et al. (1998) Mol Cell Biol 9:3273-3297.] These data were re-analyzed in: (1) Zhao LP, et al. (2001) Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc Natl Acad Sci U S A 98(10):5631-6. View data, and (2) Alter O, Brown PO, Botstein D (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97(18):10101-6. View data.
A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila et al. (in press). This includes access to three new expression data sets generated using spotted
cDNA arrays after sampling alpha factor synchronized cells across a time-course. Two of these data sets and three additional data sets from the public domain have been analyzed using a permutation based method
published by de Lichtenberg et al. (2005) Bioinformatics 21:1164-71 to calculate a weighted average peak time base. This interactive resource allows users to sort and filter data, as well as access expression plots and heat maps.
a database containing most of the published
yeast microarray expression datasets as described in Marc et al. (2001) Nucleic Acids Res 29(13):e63
a software tool for interpretation of microarray expression datasets
a Visual Basic application that displays expression data on biochemical
and cellular pathways as well as groups of genes. MAPPFinder is a related tool that integrates GO
annotations with GenMAPP to create a global expression profile
(see Doniger et al. (2003) Genome Biology 4:R7)
homepage for Serial Analysis of Gene Expression project at Johns Hopkins University
Localization Data Resources
S. cerevisiae protein localization data from
University Graz. Users may also submit
images.
Yeast transposon tagging data from the Yale Genome Analysis Center.
A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae
S. cerevisiae protein localization data
from the laboratories of Erin O'Shea and Jonathan Weissman at
the University of California San Francisco.
Phenotype Data Resources
A chemical genomics phenotype database to query for
phenotypes of href="#deletions yeast deletion strains] grown in the presence of triterpene glycosides (TTG's) from
the cactus Stenocereus gummosus (common name
agria). Pre-publication access provided by Scott Erdman at
Syracuse University.
A collection of micrographs of budding yeast mutants. For more
information, please refer to [http:www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000075221 Saito et al. (2004) Nucleic Acids Res 32:D319-22.]
A database that provides quantitative
information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains.
For more information, please refer to Warringer et al. (2003) Proc Natl Acad Sci USA 100:15724-9.
GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.
Additional Yeast Research Resources
Deletion strains created by the Saccharomyces Genome Deletion project] are available via ATCC (online catalog available), Open Biosystems, and Invitrogen (Research Genetics). The Community Posting Page provided by the Saccharomyces Genome Deletion Project enables users of the mutant collection to share information about the collection. EUROSCARF makes deletion strains available from the EUROFAN projects.
Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]
A colloboration between the Sanger Institute and Prof. Ed Louis' group at the
Institute of Genetics, University of Nottingham to analyze sequences from multiple strains of S. cerevisiae and S. paradoxus.
Promotes the study of S. cerevisiae systems biology by facilitating
cooperation between experimental scientists and theoreticians,
generating quantitative data, and developing new resources. Download YSBN's
[http:www.yeastgenome.org/community/ysbn.pdf brochure] for more information and contacts.
Repository and distributor of plasmid
constructs described in published literature. Search for a plasmid or deposit your plasmid to the repository.
Other Resources
Developed by OpenHelix, this online tutorial describes navigation of SGD and many features of the database.
Gene Ontology (GO) Consortium home page
metabolic reactions and pathways from Kyoto University, Kyoto, Japan
resources from CMS. An impressive set of hyperlinks with a great presentation on all aspects of molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling.
provided by the Harvard Biolabs
The Microbiology Information Portal. This site
contains resources, news, and information about many different aspects
of microbiology. Its General Microbiology section contains links to various databases, culture
collections, genetic analysis sites, and method sites.
a collection of articles on a wide variety of biological topics, from the Nature Publishing Group
list of WWW biological information resources
A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.
Nucleic Acids Research Database Issues
articles about genomic and biological databases
Go to NAR Database Issue for:
2008 |
2007 |
2006 |
2005 |
2004 |
2003 |
2002 |
2001 |
2000 |
1999 |
1998 |
View SGD's article] for:
2008 |
2007 |
2006 |
2005|
2004 |
2003 |
2002 |
2001 |
2000 |
1999 |
1998
