Accelerating Metagenomics Using Graphics Processing Units

Award Information
Agency:
Department of Energy
Branch
n/a
Amount:
$99,605.00
Award Year:
2010
Program:
STTR
Phase:
Phase I
Contract:
n/a
Award Id:
95220
Agency Tracking Number:
95253
Solicitation Year:
n/a
Solicitation Topic Code:
35 a
Solicitation Number:
n/a
Small Business Information
21536 Saratoga heights drive, Saratoga, CA, 95070
Hubzone Owned:
N
Minority Owned:
N
Woman Owned:
N
Duns:
112719153
Principal Investigator:
Mathew Hudson
Dr.
(217) 244-8096
mhudson@uiuc.edu
Business Contact:
A Karunakaran
Mr.
(408) 378-7008
agk@multicorewareinc.com
Research Institute:
University of Illinois
Kathy Young
1901 South First Street, Suite A
South Research Park
Champaign, IL, 61820
(217) 333-2187
Nonprofit college or university
Abstract
A key application of the technological breakthrough associated with decreased cost of DNA sequencing is metagenomics. Metagenomics is the process of sequencing DNA from whole ecosystems, rather than individuals or cultures. This approach has the potential to allow the dissection of microbial ecosystems in biofuel producing agricultural land, toxic contaminated sites and hydrocarbon recovery environments, and as such is of substantial and recognized importance to DoE. The limiting technology for metagenomics is currently the huge amounts of computer power needed to process sequences and determine their origin. The overall objective of this proposal is to develop software for metagenomic sequence analysis which takes advantage of the computing power of graphics processing units (GPUs) using CUDA, a programming interface allowing rapid development of software which utilizes the processing power of the GPU for applications other than graphics. Commercial Applications and Other Benefits: The advantage of sequence analysis software which runs on GPUs is that it will run at much higher speeds than currently available on inexpensive computer hardware. By making this software commercially available we will produce a product which will make DNA sequence analysis much more affordable, both for metagenomics and other applications.

* information listed above is at the time of submission.

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