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  1. EcoCyc (View Publication)
    Full Name of the Resource : E. coli K12 genes, pathways, transporters, and gene regulation
    Resource Category : Databases -> Genomic Databases (Non-Human) -> Escherichia coli

    Brief Description : EcoCyc is a model organism database that describes the genome and the biochemical network of E. coli K-12. EcoCyc version 12.1 (June 2008) integrates the annotated E. coli genome sequence with a rich collection of information curated from more than 17,000 publications. The database describes each E. coli gene and its gene product. The EcoCyc project closely monitors the biochemical literature and incorporates newly determined E. coli gene functions into EcoCyc. Metabolic and signaling pathways are described as interconnected sets of biochemical reactions. Transport processes are encoded as reactions whose substrates are labeled with the compartments they span. Mechanisms of gene regulation are also encoded as sequences of molecular interactions, such as binding of a transcription factor to its complementary DNA site. EcoCyc users employ the Pathway Tools software to query and visualize information within EcoCyc. The software produces intuitive drawings of pathways, operons, biochemical reactions, transport processes, and includes a genome browser. The software also produces visualizations of the entire metabolic map and regulatory network of E. coli. Gene expression and other \'omics datasets can be painted onto those diagrams for analysis. EcoCyc is available through the WWW at the URL provided. It is also available as a binary program for local installation on the Macintosh, PC, and Linux, and as a set of flat files.
    Subject Area : Escherichia coli Genomics


    Institute/s :
    Bioinformatics Research Group SRI International Menlo Park, CA 94025, USA

    Country : Mexico

    Associated Institutes :

    • SRI International, 333 Ravenswood Ave., Menlo Park, CA 94025, USA
    • Programa de Genomica Computacional, Centro de Ciencias Genomics, Universidad Nacional Autónoma de Mexico
    • Cuernavaca, Morelos, 62100, Mexico
    • Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
    • Department of Microbiology, Immunology, and Molecular Genetics
    • UCLA Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA

    Associated Country : USA; Mexico; Australia


    Authors/Contributors : P.D. Karp
    Contact Email : pkarp@ai.sri.com
    Year : 2001
    Language : English