SECOND GENERATION DNA SEQUENCE MANAGEMENT TOOLS

Award Information
Agency: Department of Health and Human Services
Branch: N/A
Contract: 2R44HG002244-02
Agency Tracking Number: HG002244
Amount: $1,091,651.00
Phase: Phase II
Program: SBIR
Awards Year: 2002
Solicitation Year: N/A
Solicitation Topic Code: N/A
Solicitation Number: N/A
Small Business Information
GEOSPIZA, INC.
GEOSPIZA, INC., 3939 LEARY WAY, NW, SEATTLE, WA, 98107
DUNS: N/A
HUBZone Owned: N
Woman Owned: N
Socially and Economically Disadvantaged: N
Principal Investigator
 TODD SMITH
 (206) 633-4403
 TODD@GEOSPIZA.COM
Business Contact
 TODD SMITH
Phone: (206) 633-4403
Email: TODD@GEOSPIZA.COM
Research Institution
N/A
Abstract
The human genome project spurred the development of high throughput technologies, especially in the area of DNA sequencing. Not only has this effort produced a draft of the human genome, it's catalyzed development of an entire industry based on DNA sequencing and genomics. Since these technologies produce enormous amounts of data they depend on bioinformatics programs for data management. Phrap, Cross_Match, RepeatMasker and Consed are four programs that played an integral role in the human genome project and became accepted as standard. However, as the technology for sequencing has evolved, so too, have the applications. These new applications include sequencing additional genomes, EST cluster analysis, and genotyping and they have highlighted the need to update standard bioinformatics programs to meet the current needs of a broader community. In this project we will re-engineer Phrap, Cross_Match and Repeat Masker to improve performance by optimizing these algorithms and developing a hierarchical data file to store and manipulate assembled sequence data. Phrap and Cross_Match will also be modified to use XML-formatted data allowing users to apply constraints to sequence assembly. Lastly, we will develop a new program to review, edit, and manipulate sequences, thus giving users unprecedented control over their data.

* information listed above is at the time of submission.

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