Web site and design © 2008 by G6G Consulting Group. All Rights Reserved. Most product content has been taken directly from manufacturer's web sites;
other product content is assembled by G6G Consulting Group. G6G welcomes any corrections and/or comments.
Product Feedback
* Required Field
*Your name:
*Email:
*Questions, comments, or feedback:
    Bioinformatics Toolbox 3.0

    Category  Genomics>Gene Expression Analysis/Profiling/Tools

    Abstract  Bioinformatics Toolbox 3.0 offers computational molecular
    biologists and other research scientists an open and extensible
    environment in which to explore ideas, prototype new algorithms, and
    build applications in drug research, genetic engineering, and other
    genomics and proteomics projects. The toolbox provides access to
    genomic and proteomic data formats, analysis techniques, and
    specialized visualizations for genomic and proteomic sequence and
    microarray analysis. Most functions are implemented in the open
    MATLAB (see Note 1) language, enabling you to customize the
    algorithms or develop your own. Key features include:

    Microarray Data Analysis and Visualization - Product enables you to
    analyze and comprehend raw microarray data.

    Microarray Normalization - You can use several methods for
    normalizing microarray data, including lowess, global mean, median
    absolute deviation (MAD), and quantile normalization. You can apply
    these methods to the entire microarray chip or to specific regions or
    blocks. Filtering and imputation functions let you clean raw data before
    running analysis and visualization routines.

    Data Analysis and Visualization - Bioinformatics Toolbox lets you
    perform background adjustment and calculate gene (probe set)
    expression values from Affymetrix microarray probe-level data using
    robust multiarray average (RMA) and guanine-cytosine robust
    multiarray average (GCRMA). You can apply circular binary
    segmentation (CBS) to array comparative genomic hybridization (CGH)
    data and estimate the false discovery rate (FDR) of multiple
    hypotheses testing of gene expression data from a microarray
    experiment. You can perform rank-invariant set normalization on either
    probe intensities for multiple Affymetrix CEL (cell intensity) files or gene
    expression values from two different experimental conditions.

    Specialized routines for visualizing microarray data include volcano
    plots, box plots, loglog plots, I-R plots, and spatial heat maps of the
    microarray. You can also visualize ideograms with G-banding (Giemsa
    stain-banding) patterns.

    Using routines from Statistics Toolbox (required, and available
    separately - see Note 2), you can classify your results, perform
    hierarchical and K-means clustering, and represent your microarray
    data in statistical visualizations, such as two-dimensional
    clustergrams with optimal leaf ordering, heat maps, principle
    component plots, and classification trees.

    Additional Key Features include:
    1) Support for mass spectrometry preprocessing and analysis.
    2) Graph theory and graph visualization tools.
    3) Statistical learning functionality.
    4) Gene Ontology (GO) functionality.
    5) Sequence analysis tools including functions for pairwise and
    multiple sequence alignment.
    6) Phylogenetic tree analysis tools.
    7) Genomic, proteomic, and gene expression file formats.
    8) Access to Web-based databases.

    Note 1: MATLAB is a high-level language and interactive environment
    that enables you to perform computationally intensive tasks faster than
    with traditional programming languages such as C, C++, and
    FORTRAN.

    Note 2: Statistics Toolbox extends MATLAB to support a wide range of
    common statistical tasks. The toolbox contains two (2) categories of
    tools - 1) Building-block statistical functions for use in MATLAB
    programming; 2) Graphical user interfaces (GUIs) for interactive data
    analysis.

    System Requirements  

    Product Requirements
    Requires MATLAB
    Optimization Toolbox recommended
    Not available on Windows x64, Solaris 64

    General System Requirements for
    Windows
    Linux
    Solaris
    Mac  

    Manufacturer   Home office; see web site for international locations.

    The MathWorks, Inc.
    3 Apple Hill Drive
    Natick, MA 01760-2098
    USA
    Phone: 508-647-7000
    Fax: 508-647-7001
The G6G Directory of Omics and Intelligent Software
Search www.G6G-SoftwareDirectory.com