Searching Biological Sequence Databases Using Distributed Adaptive Computing

Genetic research projects currently can require enormous computing power to processes the vast quantities of data available. Further, DNA sequencing projects are generating data at an exponential rate greater than that of the development microprocessor technology; thus, new, faster methods and techniques of processing this data are needed. One common type of processing involves searching a sequence database for the most similar sequences. Here we present a distributed database search system that utilizes adaptive computing technologies. The search is performed using the Smith-Waterman algorithm, a common sequence comparison algorithm. To reduce the total search time, an initial search is performed using a version of the algorithm, implemented in adaptive computing hardware, which is designed to efficiently perform the initial search. A final search is performed using a complete version of the algorithm. This two-stage search, employing adaptive and distributed hardware, achieves a performance increase of several orders of magnitude over similar processor based systems.

Name thesis:degree_name

Master of Science

Level thesis:degree_level

masters

Discipline thesis:degree_discipline

Computer Engineering

Department dc:contributor.department

Electrical and Computer Engineering

Grantor dc:publisher

Virginia Tech

Year dc:date.issued

2003

Author dc:creator

• Pappas, Nicholas Peter

Chair dc:contributor.committeechair

• Athanas, Peter M.

Committee members dc:contributor.committeemember

• Dickerman, Allan W.
• Hsiao, Michael S.
• Jones, Mark T.

• bioinformatics
• Smith-Waterman algorithm
• adaptive computing
• configurable computing
• sequence comparison
• sequence alignment
• Field programmable gate arrays

Statement dc:rights

• In Copyright

Licence dc:rights.uri

• http://rightsstatements.org/vocab/InC/1.0/

Dc Identifier Other

etd-01302003-145726

OAI identifier oai:identifier

oai:vtechworks.lib.vt.edu:10919/31074