External Links

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*[http://www.ncbi.nlm.nih.gov/genbank/ GenBank] sequence repository at the  [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA
 
*[http://www.ncbi.nlm.nih.gov/genbank/ GenBank] sequence repository at the  [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA
  
*[http://www.ebi.ac.uk/ena/ EMBL] sequence repository at the  [http://www.ebi.ac.uk/ EBI], Hinxton Hall, Cambridge, UK
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*[http://www.ebi.ac.uk/ena/ ENA (European Nucleotide Archive)] sequence repository at the  [http://www.ebi.ac.uk/ EMBL-EBI], Hinxton Hall, Cambridge, UK
  
 
*[http://www.nig.ac.jp/english/index.html DDBJ] sequence repository at Mishima, Japan
 
*[http://www.nig.ac.jp/english/index.html DDBJ] sequence repository at Mishima, Japan
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*[http://www.genepalette.org/GenePalette/Home.html GenePalette] software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences
 
*[http://www.genepalette.org/GenePalette/Home.html GenePalette] software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences
  
*[http://www.oridb.org OriDB] catalog of confirmed and predicted DNA replication origin sites, currently limited to <i>S. cerevisiae</i>
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*[http://www.oridb.org/index.php OriDB] catalog of confirmed and predicted DNA replication origin sites, currently limited to <i>S. cerevisiae</i>
  
*[http://seq.cbrc.jp/~wataru/PROSPECT/ PROSPECT: Promoter Inspection Tool] explore promoter regions by searching for genes or a sequence.  Also contains a list of yeast transcription factor binding sites.
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*[http://cellmontage.cbrc.jp/~wataru/PROSPECT/ PROSPECT: Promoter Inspection Tool] explore promoter regions by searching for genes or a sequence.  Also contains a list of yeast transcription factor binding sites.
  
 
*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools] search for regulatory signals in the non-coding sequences of <I>S. cerevisiae, S. pombe,</I> and other organisms
 
*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools] search for regulatory signals in the non-coding sequences of <I>S. cerevisiae, S. pombe,</I> and other organisms
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*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of <i>Saccharomyces cerevisiae</i>] 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.
 
*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of <i>Saccharomyces cerevisiae</i>] 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.
  
*[http://www2.imtech.res.in/anand/sacch_prom_pat.html Search for conserved patterns in <i>Saccharomyces</i> spp.] search tool for identification and analysis of conserved patterns in <i>Saccharomyces</i> promoters.  Formore information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079651 Kohli DK, <i>et al</i> (2004) <i>In Silico Biol</i> 4(3):0034]]
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*[http://compbio.soe.ucsc.edu/yeast_introns.html Yeast Introns] yeast intron data from the Ares Lab, U.C. Santa Cruz
 
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*[http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast Introns] yeast intron data from the Ares Lab, U.C. Santa Cruz
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*[http://people.biochem.umass.edu/fournierlab/snornadb/main.php Yeast snoRNAs] yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts
 
*[http://people.biochem.umass.edu/fournierlab/snornadb/main.php Yeast snoRNAs] yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts
  
*[http://lowelab.cse.ucsc.edu/GtRNAdb/Sacc_cere/ Yeast tRNAs] yeast tRNA information from Todd Lowe, UC-Santa Cruz
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*[http://lowelab.ucsc.edu/tRNAscan-SE/ Yeast tRNAs] yeast tRNA information from Todd Lowe, UC-Santa Cruz
  
 
=Genome and Protein Resources=
 
=Genome and Protein Resources=
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*[http://supfam.org/SUPERFAMILY/index.html Structural assignments of proteins] This website provides structural assignments to protein sequences at the superfamily level.  You can browse an  [http://supfam.org/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=sc overview] of all the superfamilies currently identified in <i>S. cerevisiae</i>; the site also provides several different ways to search this information.  See [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11697912&dopt=Abstract Gough et al.] for more information.
 
*[http://supfam.org/SUPERFAMILY/index.html Structural assignments of proteins] This website provides structural assignments to protein sequences at the superfamily level.  You can browse an  [http://supfam.org/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=sc overview] of all the superfamilies currently identified in <i>S. cerevisiae</i>; the site also provides several different ways to search this information.  See [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11697912&dopt=Abstract Gough et al.] for more information.
  
*[http://genome.wustl.edu/tools/blast/ Genome Sequence Center: BLAST Server]at the Washington University GSC in St. Louis. BLAST searches may be performed against genomic sequences from five <i>Saccharomyces</i> species: <i>S. mikatae, S. kudriavzevii, S. bayanus, S. castellii,</i> and <i>S. kluyveri</i>.
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*[http://mips.helmholtz-muenchen.de/genre/proj/yeast/ Yeast Project at MIPS] yeast information from the Munich Information Center for Protein Sequences ([http://www.helmholtz-muenchen.de/en/ibis MIPS])
  
*[http://mips.gsf.de/proj/yeast/CYGD/db/index.html Yeast Project at MIPS] yeast information from the Munich Information Center for Protein Sequences ([http://mips.gsf.de/ MIPS])
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*[http://www.biobase-international.com/product/proteome Yeast Proteome Database (YPD)] yeast protein information from Biobase. Access to this resource requires a subscription.
 
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*[http://www.incyte.com/control/tools/proteome Yeast Proteome Database (YPD)] yeast protein information from Incyte Genomics, Inc. Access to this resource requires a subscription.
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*[http://www.doe-mbi.ucla.edu/Services/GPofYPF/index.html Genome-Wide Protein Function Prediction] Links between functionally related yeast proteins are used to predict functions for about two thirds of all predicted yeast proteins in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044838 Marcotte <i>et al.</i> (1999) <i>Nature</i> 402:83-86.]
 
*[http://www.doe-mbi.ucla.edu/Services/GPofYPF/index.html Genome-Wide Protein Function Prediction] Links between functionally related yeast proteins are used to predict functions for about two thirds of all predicted yeast proteins in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044838 Marcotte <i>et al.</i> (1999) <i>Nature</i> 402:83-86.]
  
*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES - a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu  Yale Genome Analysis Center.]
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*[http://depts.washington.edu/sfields/yp_interactions/index.html Yeast Protein Linkage Map] The Fields lab's systematic Two-Hybrid project. Results are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043128 Uetz <i>et al.</i> (2000) <i>Nature</i> 403:623-627.]
  
*[http://depts.washington.edu/~sfields/yp_interactions/index.html Yeast Protein Linkage Map] The Fields lab's systematic Two-Hybrid project. Results are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043128 Uetz <i>et al.</i> (2000) <i>Nature</i> 403:623-627.]
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*[http://www.thebiogrid.org/ General Repository for Interaction Datasets (BioGRID)] 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 [http://mips.helmholtz-muenchen.de/genre/proj/yeast/ MIPS] database, and BIND.
 
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*[http://www.thebiogrid.org/ General Repository for Interaction Datasets (BioGRID)] 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 [http://mips.gsf.de/proj/yeast/CYGD/db/index.html MIPS] database, and BIND.
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*[http://biodata.mshri.on.ca/osprey/servlet/Index Osprey: A Network Visualization System] 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  [http://www.thebiogrid.org/ General Repository of Interaction Datasets (BioGRID)] and as a result brings a large dataset of interactions to your fingertips.
 
*[http://biodata.mshri.on.ca/osprey/servlet/Index Osprey: A Network Visualization System] 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  [http://www.thebiogrid.org/ General Repository of Interaction Datasets (BioGRID)] and as a result brings a large dataset of interactions to your fingertips.
  
*[http://www.yeastrc.org/pdr/ Yeast Resource Center Public Data Repository] 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 <i>S. cerevisiae</i> proteins.  Please see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15608220 Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82] for more information.
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*[http://www.yeastrc.org/pdr/pages/front.jsp Yeast Resource Center Public Data Repository] 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 <i>S. cerevisiae</i> proteins.  Please see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15608220 Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82] for more information.
  
 
*[http://gpmdb.thegpm.org/gpmdb_help.html The Global Proteome Machine Database (GPMDB)] a database of mass spectrometry based proteomics information, populated by the general proteomics community.
 
*[http://gpmdb.thegpm.org/gpmdb_help.html The Global Proteome Machine Database (GPMDB)] a database of mass spectrometry based proteomics information, populated by the general proteomics community.
  
*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Order Browser] a tool used to visualize the syntenic context of any gene from <i>S. cerevisiae</i>, <i>S. castellii</i>, <i>C. glabrata</i>, <i>A. gossypii</i>, <i>K. lactis</i>, <i>K. waltii</i>, and <i>S. kluyveri</i>. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113653 Byrne and Wolfe].
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*[http://ygob.ucd.ie/ Yeast Gene Order Browser] a tool used to visualize the syntenic context of any gene from <i>S. cerevisiae</i>, <i>S. castellii</i>, <i>C. glabrata</i>, <i>A. gossypii</i>, <i>K. lactis</i>, <i>K. waltii</i>, and <i>S. kluyveri</i>. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113653 Byrne and Wolfe].
 
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*[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/index.shtml YOGY:eukarYotic OrtholoGY] a tool to view orthologous proteins from eukaryotic orgranisms (<i>Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe</i>, and <i>Saccharomyces cerevisiae</i>). This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL and manually curated orthologs between <i>S. cerevisiae </i> and <i>S. pombe</i>. This tool was developed by [http://www.sanger.ac.uk/PostGenomics/S_pombe/ Penkett CJ, Morris JA, Wood V, and Bahler J] (Wellcome Trust Sanger Institute, Cambridge, UK).
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*[http://www.binofo.com/en/bioinformatics/iproto/ iProto Yeast] an iPhone application containing proteome information for several different <i>Saccharomyces</i> and <i>Schizosaccharomyces</i> strains
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*[http://refnucl.atlas.bx.psu.edu/ Yeast Nucleosome Positions] a compiled and systematic reference map of nucleosome positions across the <i>S. cerevisiae</i> genome
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*[http://128.40.79.33/YOGY/ YOGY:eukarYotic OrtholoGY] a tool to view orthologous proteins from eukaryotic orgranisms (<i>Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe</i>, and <i>Saccharomyces cerevisiae</i>). This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL and manually curated orthologs between <i>S. cerevisiae </i> and <i>S. pombe</i>. This tool was developed by [http://www.sanger.ac.uk/PostGenomics/S_pombe/ Penkett CJ, Morris JA, Wood V, and Bahler J.]
  
 
*[http://interologfinder.org/simpleIfWS?operation=doStart InterologFinder]  A database of conserved and predicted novel protein-protein interactions (interologs or interologues) in human, mouse, fly, worm, and yeast based on interaction of orthologous proteins found in the other organisms. For more information please see [http://www.ncbi.nlm.nih.gov/pubmed/20353594 Wiles et al., (2010) BMC Syst Biol. Mar 30;4:36.].
 
*[http://interologfinder.org/simpleIfWS?operation=doStart InterologFinder]  A database of conserved and predicted novel protein-protein interactions (interologs or interologues) in human, mouse, fly, worm, and yeast based on interaction of orthologous proteins found in the other organisms. For more information please see [http://www.ncbi.nlm.nih.gov/pubmed/20353594 Wiles et al., (2010) BMC Syst Biol. Mar 30;4:36.].
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=Expression Data Resources=
 
=Expression Data Resources=
  
*[http://www.yeastract.com/ YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking)] A curated database of regulatory associations between transcription factors and their target genes, and information on transcription factor binding sites (see [http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D132 Monteiro <i>et al.</i></a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).  
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*[http://www.yeastract.com/ YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking)] A curated database of regulatory associations between transcription factors and their target genes, and information on transcription factor binding sites (see [http://nar.oxfordjournals.org/content/36/suppl_1/D132.full Monteiro <i>et al.</i></a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).  
  
*[http://sceptrans.org/ SCEPTRANS] A website for visualizing and studying periodic transcription in yeast (see  [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000122214  Kudlicki et al. (2007) Bioinformatics])  
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*[http://moment.utmb.edu/cgi-bin/sceptrans.cgi SCEPTRANS] A website for visualizing and studying periodic transcription in yeast (see  [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000122214  Kudlicki et al. (2007) Bioinformatics])  
  
*[http://genome-www.stanford.edu/cellcycle/ Yeast Cell Cycle Analysis Projects] Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman <i>et al.</i> (1998) <i>Mol Cell Biol</i> 9:3273-3297.]  These data were re-analyzed in: (1)  [http://www.pnas.org/cgi/content/full/98/10/5631 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. [http://www.fhcrc.org/science/labs/breeden/spm/ View data], and (2)  [http://www.yeasgenome.org/cgi-bin/reference/reference.pl?dbid=S000060075 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. [http://genome-www.stanford.edu/SVD/ View data].
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*[http://genome-www.stanford.edu/cellcycle/ Yeast Cell Cycle Analysis Projects] Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman <i>et al.</i> (1998) <i>Mol Cell Biol</i> 9:3273-3297.]  These data were re-analyzed in: (1)  [http://www.pnas.org/content/98/10/5631.full 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. [http://labs.fhcrc.org/breeden/spm/ View data], and (2)  [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000060075 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. [http://genome-www.stanford.edu/SVD/htmls/pnas.html View data].
  
*[http://www.fhcrc.org/science/labs/breeden/cellcycle/ Periodic Genes of the Yeast <i>Saccharomyces cerevisiae</i>] A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila <i>et al.</i> (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  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15513999&dopt=Abstract de Lichtenberg et al. (2005) <i>Bioinformatics</i> 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.
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*[http://labs.fhcrc.org/breeden/cellcycle/ Periodic Genes of the Yeast <i>Saccharomyces cerevisiae</i>] A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila <i>et al.</i> (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  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15513999&dopt=Abstract de Lichtenberg et al. (2005) <i>Bioinformatics</i> 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.
  
*[http://www.transcriptome.ens.fr/ymgv/ Yeast Microarray Global Viewer] a database containing most of the published yeast microarray expression datasets as described in  [http://nar.oxfordjournals.org/cgi/content/abstract/29/13/e63 Marc<i> et al.</i> (2001) <i>Nucleic Acids Res</i> 29(13):e63]  
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*[http://www.transcriptome.ens.fr/ymgv/ Yeast Microarray Global Viewer] a database containing most of the published yeast microarray expression datasets as described in  [http://nar.oxfordjournals.org/content/29/13/e63.abstract Marc<i> et al.</i> (2001) <i>Nucleic Acids Res</i> 29(13):e63]  
  
 
*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays] a software tool for interpretation of microarray expression datasets  
 
*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays] a software tool for interpretation of microarray expression datasets  
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= Localization Data Resources=
 
= Localization Data Resources=
  
*[http://images.yeastrc.org/ Yeast Resource Center Public Image Repository (YRC PIR)] Very large repository of images and metadata from fluorescence microscopy experiments, including localization, colocalization and FRET experiments. Mostly contains data from <i>S. cerevisiae</i>, but also currently includes some <i>S. pombe</i>. Submission of data is welcome and encouraged. Please see [http://www.ncbi.nlm.nih.gov/pubmed/20482811 Riffle <i>et al</i> (2010)] for more information.
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*[http://images.yeastrc.org/imagerepo/searchImageRepoInit.do Yeast Resource Center Public Image Repository (YRC PIR)] Very large repository of images and metadata from fluorescence microscopy experiments, including localization, colocalization and FRET experiments. Mostly contains data from <i>S. cerevisiae</i>, but also currently includes some <i>S. pombe</i>. Submission of data is welcome and encouraged. Please see [http://www.ncbi.nlm.nih.gov/pubmed/20482811 Riffle <i>et al</i> (2010)] for more information.
  
 
*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)] <i>S. cerevisiae</i> protein localization data from University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit] images.
 
*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)] <i>S. cerevisiae</i> protein localization data from University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit] images.
  
*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES- a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the  [http://ygac.med.yale.edu  Yale Genome Analysis Center.]
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*[http://wardlab.cbs.umn.edu/yeast/ Yeast Membrane Protein Library] A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from <i>S. cerevisiae</i>
 
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*[http://www.cbs.umn.edu/yeast/ Yeast Membrane Protein Library] A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from <i>S. cerevisiae</i>
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*[http://yeastgfp.yeastgenome.org/ Yeast GFP Fusion Localization Database] <i>S. cerevisiae</i> protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.
 
*[http://yeastgfp.yeastgenome.org/ Yeast GFP Fusion Localization Database] <i>S. cerevisiae</i> protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.
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=Phenotype Data Resources=
 
=Phenotype Data Resources=
  
*[http://syllabus.syr.edu/bio/seerdman/TTG/ Agria Triterpene Glycoside (TTG) Phenotype Query Page] 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 <i>Stenocereus gummosus</i> (common name agria). Pre-publication access provided by Scott Erdman at Syracuse University.
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*[http://scmd.gi.k.u-tokyo.ac.jp/datamine/ The Saccharomyces Cerevisiae Morphological Database (SCMD)] 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 <i>et al.</i> (2004) <i>Nucleic Acids Res</i> 32:D319-22.]
 
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*[http://yeast.gi.k.u-tokyo.ac.jp/ The Saccharomyces Cerevisiae Morphological Database (SCMD)] 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 <i>et al.</i> (2004) <i>Nucleic Acids Res</i> 32:D319-22.]
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*[http://prophecy.lundberg.gu.se/ PROPHECY] A database that provides quantitative information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000119344 Warringer et al. (2003) <i>Proc Natl Acad Sci USA</i> 100:15724-9.]
 
*[http://prophecy.lundberg.gu.se/ PROPHECY] A database that provides quantitative information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000119344 Warringer et al. (2003) <i>Proc Natl Acad Sci USA</i> 100:15724-9.]
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*[http://genomics.senescence.info/genes/models.html GenAge] GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.
 
*[http://genomics.senescence.info/genes/models.html GenAge] GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.
  
=Genetic Interactions Resources=
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=Interactions Resources=
  
 
*[http://drygin.ccbr.utoronto.ca/ DRYGIN] A database of quantitative genetic interactions of ''S. cerevisiae'' derived from the SGA double-mutant arrays conducted in Boone lab at Terrence Donnelly Centre for Cellular and Biochemical Research, University of Toronto.
 
*[http://drygin.ccbr.utoronto.ca/ DRYGIN] A database of quantitative genetic interactions of ''S. cerevisiae'' derived from the SGA double-mutant arrays conducted in Boone lab at Terrence Donnelly Centre for Cellular and Biochemical Research, University of Toronto.
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*[http://www.esyn.org esyN] A web-tool to visualize, build, and analyze protein and gene interaction networks. Currently used by [http://www.flymine.org/flymine/begin.do flymine.org] to display interactions on their site.
  
 
=Literature Resources=
 
=Literature Resources=
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=Additional Yeast Research Resources=
 
=Additional Yeast Research Resources=
  
*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains] Deletion strains created by the <i>Saccharomyces</i> Genome Deletion project] are available via  [http://www.atcc.org ATCC] ([http://www.atcc.org/catalog/all/allIndex.cfm online catalog] available), [http://www.openbiosystems.com/ Open Biosystems], and [http://mp.invitrogen.com/ Invitrogen] (Research Genetics).  The [http://www-sequence.stanford.edu/group/yeast_deletion_project/gb/ykocp.html Community Posting Page] provided by the  [http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Saccharomyces Genome Deletion Project] enables users of the mutant collection to share information about the collection. [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/ EUROSCARF] makes deletion strains available from the EUROFAN projects.
+
*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains] Deletion strains created by the <i>Saccharomyces</i> Genome Deletion project] are available via  [http://www.atcc.org ATCC] ([http://www.atcc.org/en/Products/Cells_and_Microorganisms/Fungi_and_Yeast.aspx online catalog] available), [http://www.thermoscientificbio.com/openbiosystems/?redirect=true Open Biosystems], and [http://www.invitrogen.com/site/us/en/home/brands/Invitrogen.html Invitrogen] (Research Genetics).  The [http://www-sequence.stanford.edu/group/yeast_deletion_project/gb/ykocp.html Community Posting Page] provided by the  [http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Saccharomyces Genome Deletion Project] enables users of the mutant collection to share information about the collection. [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/ EUROSCARF] makes deletion strains available from the EUROFAN projects.
  
*[http://depts.washington.edu/~yeastrc/index.html NCRR Yeast Resource Center] Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]
+
*[http://depts.washington.edu/yeastrc/index.html NCRR Yeast Resource Center] Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]
  
*[http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ The Saccharomyces Genome Resequencing Project (SGRP)] A colloboration between the [http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ Sanger Institute] and [http://www.nottingham.ac.uk/genetics/people/louis/index.php?from=genContact&ID=205&S=Yeast%20Genomic%20Resources Prof. Ed Louis' group] at the Institute of Genetics, University of Nottingham to analyze sequences from multiple strains of <i>S. cerevisiae</i> and <i>S. paradoxus</i>.
+
*[http://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html The Saccharomyces Genome Resequencing Project (SGRP)] A colloboration between the [http://www.sanger.ac.uk/research/projects/genomeinformatics/ Sanger Institute] and [http://www2.le.ac.uk/colleges/medbiopsych/research/gact/resources Prof. Ed Louis' group] at the University of Leicester to analyze sequences from multiple strains of <i>S. cerevisiae</i> and <i>S. paradoxus</i>.
  
*[http://www.ysbn.org/ Yeast Systems Biology Network] Promotes the study of <i>S. cerevisiae</i> 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.
+
*[http://www.gmm.gu.se/globalysbn/  Yeast Systems Biology Network] Promotes the study of <i>S. cerevisiae</i> 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 brochure] for more information and contacts.
 
+
*[http://www.addgene.org Addgene] Repository and distributor of plasmid constructs described in published literature. [http://www.addgene.org:8080/pgvec1?f=c&cmd=showfile&file=colinfo Search] for a plasmid or [http://www.addgene.org/pgvec1?f=d&cmd=showfile&file=submit deposit] your plasmid to the repository.
+
  
 +
*[http://www.addgene.org Addgene] Repository and distributor of plasmid constructs described in published literature. [http://www.addgene.org/browse/ Search] for a plasmid or [http://www.addgene.org/deposit/add-article/ deposit] your plasmid to the repository.
  
 
=Other Resources=
 
=Other Resources=
 
*[http://www.openhelix.com/sgd SGD Tutorial] Developed by [http://www.openhelix.com/index.shtml OpenHelix], this online tutorial describes navigation of SGD and many features of the database.
 
*[http://www.openhelix.com/sgd SGD Tutorial] Developed by [http://www.openhelix.com/index.shtml OpenHelix], this online tutorial describes navigation of SGD and many features of the database.
  
*[http://www.geneontology.org Gene Ontology] Gene Ontology (GO) Consortium home page
+
*[http://www.geneontology.org/ Gene Ontology] Gene Ontology (GO) Consortium home page
  
 
*[http://www.genome.ad.jp/kegg/ KEGG] metabolic reactions and pathways from Kyoto University, Kyoto, Japan
 
*[http://www.genome.ad.jp/kegg/ KEGG] metabolic reactions and pathways from Kyoto University, Kyoto, Japan
 
*[http://restools.sdsc.edu/ Molecular Biology] 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.
 
 
*[http://mcb.harvard.edu/BioLinks.html WWW Virtual Library: Biosciences] provided by the Harvard Biolabs
 
 
*[http://www.microbes.info/ Microbes.info] The Microbiology Information Portal.  This site contains resources, news, and information about many different aspects of microbiology.  Its [http://www.microbes.info/resources/General_Microbiology/ General Microbiology] section contains links to various databases, culture collections, genetic analysis sites, and method sites.
 
  
 
*[http://www.els.net/ Encyclopedia of Life Sciences] a collection of articles on a wide variety of biological topics, from the Nature Publishing Group
 
*[http://www.els.net/ Encyclopedia of Life Sciences] a collection of articles on a wide variety of biological topics, from the Nature Publishing Group
  
*[http://dir.yahoo.com/Science/biology/ Yahoo] list of WWW biological information resources
+
*[http://dir.yahoo.com/science/biology/ Yahoo] list of WWW biological information resources
  
*[http://www.nature.com/Scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.
+
*[http://www.nature.com/scitable Scitable] 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=
 
=Nucleic Acids Research Database Issues=

Latest revision as of 21:00, 20 January 2016

Contents

[edit] General Yeast Resources

[edit] Nucleic Acid Data Resources

  • GenBank sequence repository at the NCBI, Bethesda, Maryland, USA
  • DDBJ sequence repository at Mishima, Japan
  • GenePalette software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences
  • OriDB catalog of confirmed and predicted DNA replication origin sites, currently limited to S. cerevisiae
  • Yeast Introns yeast intron data from the Ares Lab, U.C. Santa Cruz
  • Yeast snoRNAs yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts
  • Yeast tRNAs yeast tRNA information from Todd Lowe, UC-Santa Cruz

[edit] Genome and Protein Resources

  • UniProt comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
  • InterPro functional analysis of proteins through classification into families and predicting domains and important sites.
  • HomoloGene a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
  • Yeast Genome Directory A collection of papers describing the sequencing of each chromosome of the S. cerevisiae genome
  • Structural assignments of proteins 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.
  • Yeast Gene Order Browser 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.
  • YOGY:eukarYotic OrtholoGY 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.

[edit] Expression Data Resources

  • Periodic Genes of the Yeast Saccharomyces cerevisiae 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.
  • GenMAPP 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)
  • Yeast SAGE homepage for Serial Analysis of Gene Expression project at Johns Hopkins University

[edit] Localization Data Resources

  • Yeast Resource Center Public Image Repository (YRC PIR) Very large repository of images and metadata from fluorescence microscopy experiments, including localization, colocalization and FRET experiments. Mostly contains data from S. cerevisiae, but also currently includes some S. pombe. Submission of data is welcome and encouraged. Please see Riffle et al (2010) for more information.
  • Yeast Membrane Protein Library A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae
  • Yeast GFP Fusion Localization Database S. cerevisiae protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.

[edit] Phenotype Data Resources

  • GenAge GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.

[edit] Interactions Resources

  • DRYGIN A database of quantitative genetic interactions of S. cerevisiae derived from the SGA double-mutant arrays conducted in Boone lab at Terrence Donnelly Centre for Cellular and Biochemical Research, University of Toronto.
  • esyN A web-tool to visualize, build, and analyze protein and gene interaction networks. Currently used by flymine.org to display interactions on their site.

[edit] Literature Resources

  • PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
  • PMC is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM).
  • Google Scholar Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites.

[edit] Additional Yeast Research Resources

  • NCRR Yeast Resource Center Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]
  • Yeast Systems Biology Network 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 brochure for more information and contacts.
  • Addgene Repository and distributor of plasmid constructs described in published literature. Search for a plasmid or deposit your plasmid to the repository.

[edit] Other Resources

  • SGD Tutorial Developed by OpenHelix, this online tutorial describes navigation of SGD and many features of the database.
  • KEGG metabolic reactions and pathways from Kyoto University, Kyoto, Japan
  • Yahoo list of WWW biological information resources
  • Scitable A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

[edit] Nucleic Acids Research Database Issues

Articles about genomic and biological databases. Go to NAR Database Issue for:
2010| 2009 | 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

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