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    Genchek

    Category  Cross-Omics>Sequence Analysis/Tools

    Abstract  Genchek is a comprehensive, multi-platform, sequence
    analysis software package. It facilitates analysis of Expressed
    Sequence Tags (ESTs), Complete Genome, and Single Nucleotide
    Polymorphism (SNP) data. Genchek is a research information and
    experiment management tool that integrates public and proprietary
    data through a discovery workspace that provides contextual access to
    sequence analysis tools, content and services. Genchek contains an
    integral database system that can be used to access, store, organize
    and retrieve DNA, protein and vector sequences in an intuitive
    environment that offers editing, management and annotation of
    sequences. Products features/capabilities include:

    Integrated Sequence and Graphical Viewer includes - 1) Sequence as
    a single strand, double strand, translation and with annotations; 2)
    Publication quality circular and linear sequence maps via the
    manufacturers graphical viewer; 3) A graphical view of restriction maps
    that facilitates easy cloning; 4) A graphical view of Open Reading
    Frames (ORFs) in the sequence maps; 5) Imported and user defined
    sequence annotations in the graphical and sequence views.

    Basic Local Alignment Search Tool (BLAST) Suite includes - 1)
    Support for blastn, blastp, blastx, tblastn, tblastx and Batch Blast; 2)
    The ability to create customized local BLAST databases through the
    manufacturers pluggable local BLAST manager; 3) BLAST queries
    against multiple local databases; 4) A customized interface to search
    and view BLAST hits graphically; 5) Hyperlinked and downloadable
    accessions to import BLAST hits on a single click; 6) The ability to
    search the Single Nucleotide Polymorphism database (dbSNP) based
    on user defined parameters.

    Sequence Alignments includes - 1) A new Alignment Editor; 2) Align
    sequence pairs through Global and Local alignments; 3) Dot plots for
    possible alignments, and secondary structures; 4) Display alignment
    results using a user-configurable color scheme; 5) The ability to align
    multiple sequences; 6) The ability to edit and save the alignments to a
    local database; 6) The ability to save alignments in Fasta, PFAM, MSF,
    Clustal, BLC, PIR formats and associated trees in the newick format;
    7) The ability to analyze Phylogenetic relationships using the neighbor
    joining algorithm and the Unweighted Pair Group Method with
    Arithmetic mean (UPGMA).

    Electropherogram Viewer includes the ability to - 1) Import all major
    chromatogram formats (e.g. Applied Biosystems (.abi), standard
    chromatogram format (.scf), .abd); 2) Import, export and modify
    chromatograms; 3) Analyze the quality of sequence information; 4)
    Manipulate the chromatogram data for the filtering of weak signals.

    Contig (a set of overlapping DNA segments derived from a single
    genetic source) Assembly includes the ability to - 1) Automatically align
    and assemble large numbers of sequences into contigs; 2) Allow
    overlap region length selection, fragment inversion check and the
    identification of consensus regions; 3) Save contig results and export a
    contig map.

    DNA Sequence Analysis includes the ability to - 1) Retrieve sequences
    in all standard sequence formats EMBL, Genbank, FASTA, DDBJ and
    popular sequence analysis software; 2) Have feature information and
    annotations loaded automatically; 3) Monitor the quality of imported
    sequence information; 4) Import chromatograms directly from
    sequencing machines; 5) Create and manipulate sequences using
    the Sequence Editor.

    Protein Sequence Analysis includes the ability to - 1) Do reverse
    translation; 2) Do Protease digest; 3) Generate plots for Amino acid
    frequency, amino acid weights, Charge vs. pH, and by Hydrophobicity;
    4) View statistics for various physico-chemical properties of the protein
    sequence; 5) Analyze protein sequence for hydrophobicity, with helical
    wheel or beta staircase representations.

    Pattern Search includes the ability to - 1) Search for DNA patterns,
    motifs and domains; 2) Search across a sequence or entire
    experiments; 3) Create your own patterns and save them for future
    usage.

    Restriction Analysis includes the ability to - 1) Simulate a restriction
    analysis experiment; 2) Define custom enzyme sets; 3) View a cut site
    and restriction information; 4) Give you a graphical view of restriction
    endonuclease (RE) analysis for increased comprehension.

    Primer Design includes the ability to - 1) Degenerate primer design to
    amplify homologous sequences; 2) Design optimal Primers for
    Polymerase Chain Reaction (PCR) and sequencing; 3) Design
    primers unique to the entire sequence or to a selected region; 4)
    Analyze Primers for dimers and hairpins; 5) Export results in a spread
    sheet format; 6) Generate PCR products to save as oligos, for further
    analysis.

    Data Management Capabilities include the ability to - 1) Have relational
    database support to organize your experiment data; 2) Store and
    manage DNA, protein, vector sequences, Restriction Enzymes,
    Oligonucleotides and BLAST Results; 3) Have a client server
    architecture to share your data over an internal network; 4) Import and
    export data in all popular formats and share results with your
    colleagues; 5) Define user specific privileges to access data.

    Extensive web interface includes the ability to - 1) Connect to several
    public database and utilities from your application; 2) Add, delete or
    edit your own set of regularly used Uniform Resource Locators (URLs).

    Local BLAST Manager includes the ability to - 1) Create and manage
    databases and their sequences on any Server; 2) Apply powerful
    BLAST searches against multiple databases using an ordinary
    desktop or laptop computer.

    Note: See G6G Product Number 20074 for additional product info from
    this manufacturer.

    System Requirements  

    Windows:
    Supported Operating Systems: Windows 98, Windows ME, Windows
    NT, Windows 2000, Windows XP.
    Memory(RAM): Minimum - 256 MB. Recommended - 512 MB.
    Display: 1024 x 768
    Free Disk Space: Minimum - 100 MB. Recommended - 125 MB.

    Mac:
    Supported Operating Systems: Mac OS X v10.2.8 or later.
    Memory(RAM): Minimum - 256 MB. Recommended - 512 MB.
    Display: 1024 x 768
    Free Disk Space: Minimum - 100 MB. Recommended - 125 MB.

    Unix:
    Supported Operating Systems: Linux or Solaris.
    Memory(RAM): Minimum - 256 MB. Recommended - 512 MB.
    Display: 1024 x 768
    Free Disk Space: Minimum - 100 MB. Recommended - 125 MB.

    Manufacturer   Home office; see web site for international locations.

    Ocimum Biosolutions Ltd.
    6th Floor, Reliance Classic
    Road No. 1, Banjara Hills
    Hyderabad - 500 034. A.P., India
    Phone: +91-40-6662-7200
    Fax: +91-40-6662-7205
    Email: hyd@ocimumbio.com
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