You are here

SECOND GENERATION DNA SEQUENCE MANAGEMENT TOOLS

Award Information
Agency: Department of Health and Human Services
Branch: National Institutes of Health
Contract: 2R44HG002244-02
Agency Tracking Number: HG002244
Amount: $0.00
Phase: Phase I
Program: SBIR
Solicitation Topic Code: N/A
Solicitation Number: N/A
Timeline
Solicitation Year: N/A
Award Year: 2002
Award Start Date (Proposal Award Date): N/A
Award End Date (Contract End Date): N/A
Small Business Information
GEOSPIZA, INC. 3939 LEARY WAY, NW
SEATTLE, WA 98107
United States
DUNS: N/A
HUBZone Owned: No
Woman Owned: No
Socially and Economically Disadvantaged: No
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. *

US Flag An Official Website of the United States Government