Searching Biological Sequence Databases Using Distributed Adaptive Computing

dc.contributor.authorPappas, Nicholas Peteren
dc.contributor.committeechairAthanas, Peter M.en
dc.contributor.committeememberDickerman, Allan W.en
dc.contributor.committeememberHsiao, Michael S.en
dc.contributor.committeememberJones, Mark T.en
dc.contributor.departmentElectrical and Computer Engineeringen
dc.date.accessioned2014-03-14T20:31:11Zen
dc.date.adate2003-02-06en
dc.date.available2014-03-14T20:31:11Zen
dc.date.issued2003-01-24en
dc.date.rdate2004-02-06en
dc.date.sdate2003-01-30en
dc.description.abstractGenetic 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.en
dc.description.degreeMaster of Scienceen
dc.identifier.otheretd-01302003-145726en
dc.identifier.sourceurlhttp://scholar.lib.vt.edu/theses/available/etd-01302003-145726/en
dc.identifier.urihttp://hdl.handle.net/10919/31074en
dc.publisherVirginia Techen
dc.relation.haspartnpappas_thesis.pdfen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectbioinformaticsen
dc.subjectSmith-Waterman algorithmen
dc.subjectadaptive computingen
dc.subjectconfigurable computingen
dc.subjectsequence comparisonen
dc.subjectsequence alignmenten
dc.subjectField programmable gate arraysen
dc.titleSearching Biological Sequence Databases Using Distributed Adaptive Computingen
dc.typeThesisen
thesis.degree.disciplineComputer Engineeringen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.levelmastersen
thesis.degree.nameMaster of Scienceen
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