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    Kodon

    Category  Cross-Omics>Sequence Analysis/Tools

    Abstract   Kodon is a fully integrated sequence analysis platform with
    unlimited database capacity. Kodon consists of a Basic Software
    module and three (3) modules for specific applications. The main
    functionality of the modules is as follows:

    1) Kodon Basic Software: contig assembly, database and advanced
    querying, sequence editor, restriction enzyme analysis, homology
    search via Basic Local Alignment Search Tool (BLAST).

    2) Multiple Alignment, Clustering and Phylogeny: sequence selection
    from feature matrix, multiple Alignment, clustering and phylogeny
    [Unweighted Pair Group Method with Arithmetic mean (UPGMA),
    Neighbor Joining, Parsimony, Maximum Likelihood].

    3) Molecular Analysis: vector construction, primer design, frame
    analysis, RNA and protein secondary structure, pairwise matching and
    repeat analysis, motif search and physico-chemical properties
    analysis.

    4) Chromosome Mapping: side-by-side comparison of genomes and
    chromosomes, analysis of organization and functional behavior of
    genomes, chromosome annotation.

    Note: The full Kodon functionality is physically contained in the same
    program unit, which guarantees integration of the modules, a
    consistent user interface, and No tedious switching between programs.

    Kodon offers the following main features:

    1) Fully integrated analysis platform, from raw sequencer
    chromatograms to megabase sequences, with full back-tracking
    functionality.

    2) GenBank and EMBL are Kodon’s native formats. No conversion, No
    loss of features and qualifiers from documented sequences.

    3) Project-oriented multi-user database environment; unlimited
    capacity. Choice between local, file-based databases and server-
    based Oracle, PostgreSQL, Microsoft SQL Server, Access, and other
    database engines. A possibility to connect to existing databases.

    4) Storage and full analysis capability on local computers. No need to
    upload data over the Internet, avoiding network traffic, enhancing data
    security, and ensuring faster return of results.

    5) Automatic updates of databases from public servers.

    6) Advanced structured queries of any complexity for searches in local
    or external databases.

    7) Rich and uniform sequence annotation display in all analysis tools:
    vector cloning, ligation, primer design, alignment, homology search,
    match and repeat analysis, etc.

    8) Feature matrix to search and select related features out of
    chromosome sequences and analyze them by multiple alignment and
    clustering.

    9) Chromosome dot plot matrix to visualize homologous regions in
    and between chromosomes. Automatic search for repeats and
    duplicates to locate paralogous and orthologous genes.

    10) In-silico cloning and restriction analysis with unparalleled
    functions and rich, publication-ready output possibilities. Simulation of
    agarose gels with restriction fragment patterns and size markers.

    11) Primer design on sequences, chromosomes, and multiple
    alignments of DNA or protein sequences. Temperature and
    degeneration plots, search for distinctive primers for Polymerase
    Chain Reaction (PCR) detection, and many other features.

    12) Prediction of RNA and protein secondary structure, helical wheel
    analysis, motif search, prediction of Leucine zippers, and physico-
    chemical property analysis.

    13) One of the finest multiple alignment editor that exists, offering a
    wealth of alignment, clustering and phylogenetic inference functions.

    14) Computationally intensive tasks such as multi-chromosome
    mapping run in background threads which can be interrupted and
    resumed whenever desired.

    15) Script language for automation of tasks, import & export,
    generation of custom reports, personalization of interface, etc.

    Note: See G6G Product Number 20010 for additional product info from
    this manufacturer.

    System Requirements  Network Licenses of Kodon

    Powerful network license solution! Compatible with Windows NT,
    Windows 2000 and Windows XP. See also the detailed description of
    the network licensing system.

    License limits. Network licenses with attractive prices are available for
    any number of users. Contact manufacturer for details and pricing.

    Manufacturer   Home office; see web site for international locations.

    Applied Maths, Inc.
    Keistraat 120, 9830 St-Martens-Latem, Belgium
    +32 9 2222 100
    13809 Research Blvd, Suite 645, Austin, TX 78750, U.S.A.
    +1 512 482 9700
    info@applied-maths.com

    Manufacturer's Web Site  www.applied-maths.com/kodon/kodon.htm

    Price  Contact manufacturer

    G6G Product Number  20070

    G6G Manufacturer Number  100308
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