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 Abstract 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

• 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

Manufacturer Web Site Affymetrix, Inc.

Price Contact manufacturer.

G6G Abstract Number 20072

G6G Manufacturer Number 100120