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    Affymetrix GeneChip  Sequence Analysis Software
    (GSEQ) Version 4.0

    Category  Cross-Omics>Sequence Analysis/Tools

    Abstract  Affymetrix GeneChip Sequence Analysis Software (GSEQ)
    4.0 is an evolution from GeneChip DNA Analysis Software (GDAS) 3.0
    and builds on the high-quality base calling and streamlined data
    analysis of GDAS 3.0. GSEQ 4.0 enables scientists to perform
    comparative sequencing by providing high quality sequence
    information and automatic detection of Single Nucleotide
    Polymorphism (SNP) sites in a single analysis package.

    Products features/benefits include:

    Automated Base Calling -
    GSEQ 4.0 provides automatic base calls by employing a unique
    algorithm derived from the work of Cutler, et al. The benefits include: 1)
    Automatic base calling of both heterozygotes and homozygotes; 2) Call
    Rates >90 percent; 3) High base-calling accuracy (>99.9 percent); 4)
    High reproducibility (>99.9 percent); 5) Automatic SNP detection and
    generation of SNP summary report.

    Streamlined Workflow -
    GSEQ displays sequence information in both tabular and graphic
    modes. The Sequence Viewer enables visualization of the sequence
    across multiple samples. Non-reference positions are automatically
    highlighted, allowing scientists to view sequence variations at a global
    level or zoom in on a particular fragment for detailed analysis. While
    viewing putative SNP positions, researchers can also view associated
    probe intensity data and edit the base calls as needed. The SNP
    Viewer provides a summary of all SNP sites across multiple samples.
    Also, sequence data and SNP sets can be exported as FASTA format
    or tab-delimited text files for downstream analysis.

    Additional features/benefits include:

    1) Reporting of Call Rate by sample and by individual fragment.

    2) Automatic assignment of base calls with editing and edit tracking.

    3) Detailed analysis of No-Calls through display of Force Call and No
    Call criteria.

    4) Alignment and display of sequences from multiple samples.

    5) Display of genomic positions and Polymerase Chain Reaction
    (PCR) start/stop positions.

    6) SNP Viewer with graphical display summarizing SNP calls by
    samples at SNP sites.

    7) Trace view of probe intensities in the context of adjacent bases

    8) File Sets allows customized groupings of samples from multiple
    projects.

    GSEQ 4.0 provides an integrated analysis workflow to enable high-
    content, high throughput, and accurate sequencing applications. In
    addition, by using the GeneChip Operating Software (GCOS)
    Database, scientists can conveniently manage data and experiment
    information at the desktop level, thus eliminating the cost of supporting
    a separate database product.

    GSEQ 4.0 Additional Specifications:

    Data Input -
    1) Cell intensity (.CEL) files from GCOS managed within the GCOS
    Process Database.
    2) GeneChip CustomSeq Library files.

    Reports and File Output -
    1) Resequencing summarized expression values (CHP files).
    2) Algorithm Report.
    3) SNP Report.

    Algorithm -
    1) Resequencing Algorithm Version 1 for 20μm x 25μm CustomSeq
    arrays.
    2) Resequencing Algorithm Version 2 for 8μm CustomSeq arrays.

    Note: See G6G Product Number 20001 for additional product info from
    this manufacturer.

    System Requirements  

    You can use GSEQ 4.0 with:

    • A stand-alone process database installed on your computer
    • A remote GCOS Server database on a network

    See your system administrator for information about using GSEQ with
    a GCOS server.

    GSEQ must be used with the GeneChip Operating System Version
    1.4 (local or Server).

    It is recommended that there is at least 500 MB of available disk
    space for the installation.

    Manufacturer   Home office; see web site for international locations.

    Affymetrix, Inc.,
    3420 Central Expressway
    Santa Clara, CA 95051
    Cust Service 888-DNA-CHIP (888-362-2447)
    Tel. 408-731-5000
    Fax. 408-731-5380
    sales@affymetrix.com
    support@affymetrix.com
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