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Searching protein sequence databases using BRBMH matching algorithm

By Ahmad Klaib and Hugh Osborne

Abstract

Huge amounts of data are stored in linear files. This is also the case for biological data. Biological proteins are sequences of amino acids. The quantities of data in these fields tend to increase year on year. For this reason efficient string-matching algorithms should be used which use minimal computer storage and which minimize the searching response time. In this paper, we propose a new algorithm called BRBMH algorithm which offers improved number of comparison and elapsed searching time when compared to the well-known algorithms such as BF, KMP, BM, BMH, KR, ZT, QS, BR, FS, SSABS, TVSBS, ZTBMH and BRFS algorithms. The experimental results show that the new algorithm is faster and perform fewer numbers of comparisons than other compared algorithms for any length of alphabets and patterns. So the proposed algorithm is applicable for searching protein sequence databases as well as in any other string searching applications

Topics: QA75, QA76
Publisher: International Journal of Computer Science and Network Security (I J C S N S)
Year: 2008
OAI identifier: oai:eprints.hud.ac.uk:9753

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