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    SciTegic Pipeline Pilot - Sequence Analysis
    Collection

    Category  Cross-Omics>Sequence Analysis/Tools

    Abstract   The Sequence Analysis Collection offers essential
    bioinformatics tools and algorithms for creating practical sequence
    analysis workflows that complement any laboratory research. With over
    100 different component functions, you can analyze and annotate DNA
    and protein sequences using a variety of industry accepted methods.
    Product can be used to combine components into logical networks
    that automate the analysis and assembly of sequence families.

    Product features/capabilities include:

    Sequence Similarity Searching - For uncomplicated sequence
    similarity searching, use the Smith-Waterman component or any of the
    products standard Basic Local Alignment Search Tool (BLAST)
    components, including BLASTn, BLASTp, BLASTx, tBLASTn, and
    tBLASTx. Display the results of these searches with the products
    Similarity Search Viewer, and extract or fetch to further analyze the
    individual hits. Pipeline Pilot (see Note 1) also makes it easy to build
    custom BLAST databases on-the-fly, providing more targeted and
    intelligent sequence similarity searches.

    Manipulation and Annotation - An assortment of sequence
    manipulation and annotation components are available. For DNA
    sequences, these components include functions such as primer
    identification, guanine-cytosine (GC) content, six-frame translations,
    reverse complement, and small interfering RNA (siRNA) target site
    prediction. For protein sequences, you can determine back translation,
    secondary structure prediction, and isoelectric point.

    Alignment and Profile Searching - To identify potential homologs
    among a collection of different organisms and quickly select variants
    among nucleotide sequence regions, you can use the products
    alignment and profiling components. To allow for multiple sequence
    alignments of either DNA or protein sequences, ClustalW (a general
    purpose multiple sequence alignment program for DNA or proteins) is
    included. For profiling tasks, hidden Markov model (HMM) Build, Align,
    Search, and Pfam (a database containing information about protein
    domains and families) are available.

    Pattern Matching - A variety of standard tools are implemented so you
    can search for interesting patterns or motifs within a biological
    sequence. These algorithms enable the identification of potential
    PROSITE (a database of protein families and domains) regions, GC
    rich regions, proteolytic cleavage sites, restriction enzyme sites, signal
    peptide cleavage sites, open reading frames, or regular expression
    patterns.

    Result Viewers - You can also visualize sequence information and
    related features with the products sequence viewers. These viewers
    include a custom report [portable document format (PDF) or hypertext
    markup language (HTML)], plain text view, or Artemis viewer (for
    nucleotide sequences). Also, multiple sequence alignments can be
    displayed in a custom report (PDF or HTML), plain text, or JalView (a
    multiple sequence alignment editor & viewer written in the Java
    programming language).

    Third-Party Tool Integration - The Sequence Analysis collection
    includes examples of integration with BioPerl, NCBI BLAST, GCG
    programs (an integrated package featuring a comprehensive
    collection of DNA-, RNA-, and protein-sequence-analysis tools),
    EMBOSS tools, and BioJava. You can use these examples as
    templates to extend the available functionality to include other
    programs of interest. Your Pipeline Pilot integration options include
    Java, Perl, Simple Object Access Protocol (SOAP), Visual Basic (VB)
    Script, or writing simple command-line wrappers.

    Note 1: Pipeline Pilot Overview - Pipeline Pilot streamlines the
    integration and analysis of vast quantities of data flooding the research
    informatics world. It makes the most of your information resources
    through industrial-scale data flow control and advanced mining
    capabilities. You can graphically compose data processing networks,
    known as 'protocols', using hundreds of different configurable
    components for operations such as data retrieval, manipulation,
    computational filtering, and display. These protocols are automatically
    captured as you create them and you can publish them for
    project/enterprise use. From a Web interface, your colleagues can
    invoke your protocols and run them using their own data, etc.

    System Requirements  

    Pipeline Pilot 6.0 or later
    Pipeline Pilot Reporting collection (for formatted output)
    Microsoft Windows with Microsoft Office (for document conversion)
    Internet access (for searching remote databases)

    Manufacturer   Home office; see web site for international locations.

    Accelrys, Inc.
    10188 Telesis Court. Suite 100
    San Diego, CA 92121-4779
    Tel: 1-858-799-5692
    Fax: 1-858- 799 5100
    support-scitegic@accelrys.com
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