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:

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:

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

System Requirements

You can use GSEQ 4.0 with:

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 Web Site Affymetrix, Inc.

Price Contact manufacturer.

G6G Abstract Number 20072

G6G Manufacturer Number 100120