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    IOGMA Metabolic Pathway Builder

    Category  Cross-Omics>Pathway Analysis/Tools

    Abstract  IOGMA Metabolic Pathway Builder is a comprehensive, fully
    integrated in-silico 'systems biology' tool kit that can be used to analyze
    and predict metabolic pathways. This advanced toolkit can be used to:
    1) Find and annotate prokaryotic sequence differences quickly and
    accurately; 2) Automatically predict protein functions directly from genes;
    3) systematically identify differences between metabolic pathways and
    map genes onto pathways.

    The Metabolic Pathway Builder integrates GenoAnnot, ProteoAnnot and
    PathwayExplorer in one package to analyze biological data from
    genome sequence to metabolic function. Metabolic Pathway Builder is
    usually linked to μB (a relational database) or to customized sets of μB
    data. This entire software integration process is accomplished through
    the Genostar IOGMA® platform.

    The Metabolic Pathway Builder offers a wide range of prokaryotic
    analysis methods. And it provides annotations from current database
    releases: GenBank, Uniprot/Swiss-Prot, TrEMBL, KEGG, Gene Ontology
    (GO), ENZYME, and Taxonomy.

    Product also allows you to transfer data and results from one IOGMA
    module to another, pursue your analysis further, and return to where you
    started. The Metabolic Pathway Builder features consistent user
    interfaces with tables, maps, and “drag-and-drop” functions across all
    modules.

    Products components/features/capabilities include:

    GenoAnnot / ProteoAnnot -- for genome annotation and comparative
    genomics giving you the ability to:
    1) Compare complete genomes or genomes as a set of contigs.
    2) Transfer annotation between genomes.
    3) Comprehensively analyze new or as-yet-unidentified genomic
    sequences using biocomputing methods and annotate those
    sequences directly.
    4) Identify regulatory signals.
    5) Predict features of polypeptide sequences.
    6) Functionally characterize coding sequences (CDS) products,
    including multiple alignments and phylogenetic reconstruction.

    PathwayExplorer -- to explore the relationships between genes, their
    enzymatic products, and metabolic pathways catalyzed by these
    enzymes, including computing and querying homologies among CDSs.

    PathwayExplorer gives you the capability to:
    1) Compare several genomes.
    2) Search for the genes that are specific to one of them.
    3) Identify the corresponding specific reactions and pathways on
    metabolic maps.
    4) Search for all the reactions which result in the chemical compounds
    described by the structure they share.
    5) Then, track back to the genes whose products catalyze these
    reactions.

    Genostar offers two (2) alternative solutions to PathwayExplorer --

    1) KEGG Explorer -- provides the same advanced capabilities of
    PathwayExplorer to apply directly to the contents of the Kyoto
    Encyclopedia of Genes and Genomes (KEGG) database. The useful
    query, navigation and display facilities of KEGG Explorer will allow you to
    make the most of your KEGG license.

    PathwayBrowser (provided with Customized Datasets) -- to query and
    display genomic, proteic and metabolic data related to a specific set of
    bacterial organisms in a Customized Dataset.

    μB Database and Customized Datasets --
    The μB Database is a relational database which integrates data from:
    1) GenomeReviews (genomic data);
    2) Swiss-Prot (proteic data);
    3) ENZYME & KEGG (metabolic data); and
    4) Gene Ontology (GO) (functional classification).

    Customized Datasets --
    Genostar bioinformaticians can extract just the data required by the
    researcher. Their quality is checked and information on enzymatic
    activity is added using dedicated prediction methods.

    IOGMA® Metabolic Pathway Builder is offered in two (2) versions:

    1) Standard Version -- consisting of: GenoAnnot; ProteoAnnot;
    PathwayExplorer; the IOGMA platform plus customized μB data subsets
    tailored to your specific research needs.

    2) Professional Version -- consisting of: the Standard Version plus the
    complete μB data on more than 450 organisms.

    Note:  a KEGG license is needed to use the IOGMA μB. Genostar can
    provide this license if it is needed.

    IOGMA Metabolic Pathway Builder Workstation(s) Configurations --

    1) Client-Server Configuration -- used to collaborate on the same
    research; the data and knowledge capture is managed on a central
    server by Oracle; and it has simultaneous access from different users;
    permitted and controlled by the IOGMA platform.

    2) Desktop Configuration -- each desktop configuration is stand-alone
    and it provides an individual workspace and data files for a single user
    ID.

    Note: See G6G Product Number 20152 for additional product info from
    this manufacturer.

    System Requirements  

    IOGMA Client Server
    Server: Linux, 4 GB RAM

    IOGMA Desktop
    Available for : Windows XP, Linux, Mac OSX
    Requires: Java 1.5.0, 512 RAM (1 GB recommended) minimum 400 MB
    free disk space

    Manufacturer   Home office; see web site for international locations.

    Genostar
    Home office: 78 bis, avenue Henri Martin, 75116 Paris France
    Sales / Service / Research & Development Group:
    60 rue Lavoisier, 38330 Montbonnot France
    Tel. +33 4 76 97 10 70
    E-mail: info@genostar.com
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