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An Optical Map-Assisted Assembler

Award Information

Agency:
Department of Health and Human Services
Branch:
N/A
Award ID:
70876
Program Year/Program:
2004 / SBIR
Agency Tracking Number:
HG003410
Solicitation Year:
N/A
Solicitation Topic Code:
N/A
Solicitation Number:
N/A
Small Business Information
GEOSPIZA, INC.
BOX 344, 2442 NW MARKET ST SEATTLE, WA 98107-
View profile »
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No
 
Phase 1
Fiscal Year: 2004
Title: An Optical Map-Assisted Assembler
Agency: HHS
Contract: 1R43HG003410-01
Award Amount: $99,767.00
 

Abstract:

DESCRIPTION (provided by applicant): Optical mapping is a method by which large-scale, efficient restriction digests can be utilized as an alternative to sequence assembly. In traditional sequence assembly, a genetic target is fragmented, amplified, and sequenced. Software algorithms then find stretches of similar sequence in sets of sequencing reads and align these sequences to each other, building consensus sequences that are intended to represent the biological genetic sequence. In optical mapping, the genetic target is subjected to a restriction digest and then imaged to appraise the length of the fragments. A key difference from other restriction techniques is that the order of the restriction fragments with respect to each other is known. A software algorithm then aligns the digested fragments of DNA to each other to generate a restriction map for the entire genetic target. We propose to design a map-assisted assembler in which the data from optical mapping are integrated into our re-engineered Phrap assembler. The optical map data will be used in the assembler to 1) verify the correctness of the assembly, 2) align assembled contigs into supertigs, and 3) prevent misassembly.

Principal Investigator:

Christie P. Robertson
2066334403
CPR@GEOSPIZA.COM

Business Contact:

Joe Hallock
2066334403
hallock@geopspiza.com
Small Business Information at Submission:

GEOSPIZA, INC.
GEOSPIZA, INC. BOX 344, 2442 NW MARKET ST SEATTLE, WA 98107

EIN/Tax ID: 911894564
DUNS: N/A
Number of Employees: N/A
Woman-Owned: No
Minority-Owned: No
HUBZone-Owned: No