Difference between revisions of "External Links"

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*[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.essaymill.com/ research papers] by research papers on-line.
*[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=

Revision as of 07:15, 23 September 2010

General Yeast Resources

  • General Yeast Topics 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.

Nucleic Acid Data Resources

  • GenBank sequence repository at the NCBI, Bethesda, Maryland, USA
  • EMBL sequence repository at the EBI, Hinxton Hall, Cambridge, UK
  • 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

  • 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.
  • 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 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 (Wellcome Trust Sanger Institute, Cambridge, UK).
  • iProto Yeast an iPhone application containing proteome information for several different Saccharomyces and Schizosaccharomyces strains

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

  • 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 Stenocereus gummosus (common name agria). Pre-publication access provided by Scott Erdman at Syracuse University.
  • GenAge GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.

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 [http:www.yeastgenome.org/community/ysbn.pdf 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.

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
  • 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.
  • Microbes.info 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.
  • 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.

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