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Rapid DNA Signature Discovery Using A Novel Parallel Algorithm

Authors:
Hsiao Ping Lee
Yen-Hsuan Huang
Tzu-Fang Sheu

Keywords: DNA signature, human chromosome EST database, parallel algorithm, unique signature discovery

Abstract:
DNA signatures provide valuable information that can be used in various applications in bioinformatics, for example the identification of different species. Rapid signature discovery algorithms are required by biologists to discover signatures. Since more and more computers are equipped with a CPU of many processing cores, parallelism becomes a feasible solution to accelerate the discovery. However, most of the existing signature discovery algorithms are sequential algorithms. Parallel signature discovery algorithms are rare. In this paper, a parallel signature discovery algorithm is proposed. The algorithm discovers hamming-distance-based signatures from DNA databases. The proposed algorithm is a parallel enhancement of an existing discovery algorithm. Through parallel computing, the algorithm accelerates the process of signature discovery. In the experiment on a human chromosome EST database of 88M bases, the proposed algorithm has up to 73.28% less processing time than the existing discovery algorithm when 4 processors are used.

Pages: 83 to 88

Copyright: Copyright (c) IARIA, 2012

Publication date: June 24, 2012

Published in: conference

ISSN: 2308-4529

ISBN: 978-1-61208-202-8

Location: Venice, Italy

Dates: from June 24, 2012 to June 29, 2012