Title page for ETD etd-01302003-145726


Type of Document Master's Thesis
Author Pappas, Nicholas Peter
Author's Email Address npappas@vt.edu
URN etd-01302003-145726
Title Searching Biological Sequence Databases Using Distributed Adaptive Computing
Degree Master of Engineering
Department Electrical and Computer Engineering
Advisory Committee
Advisor Name Title
Athanas, Peter M. Committee Chair
Dickerman, Allan W. Committee Member
Hsiao, Michael S. Committee Member
Jones, Mark T. Committee Member
Keywords
  • bioinformatics
  • Smith-Waterman algorithm
  • adaptive computing
  • configurable computing
  • sequence comparison
  • sequence alignment
  • FPGA
Date of Defense 2003-01-24
Availability unrestricted
Abstract
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.
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