General Yeast Resources
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
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.
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
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.
Phenotype Data Resources
- GenAge GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.
- 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.
- 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.
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.
- PlasmID Dana-Farber/Harvard Cancer Center (DF/HCC) DNA Resource Core, located at Harvard Medical School, is part of ORFeome Consortium. Is a distributor of open reading frame (ORF) clones for yeast and other species.
- KEGG metabolic reactions and pathways from Kyoto University, Kyoto, Japan
- 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
Articles about genomic and biological databases.
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