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Searching protein sequence databases using BRBMH matching algorithm

Klaib, Ahmad and Osborne, Hugh (2008) Searching protein sequence databases using BRBMH matching algorithm. International Journal of Computer Science and Network Security, 8 (12). pp. 410-414. ISSN 1738-7906

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    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.

    Item Type: Article
    Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
    Q Science > QA Mathematics > QA76 Computer software
    Schools: School of Computing and Engineering > Informatics Research Group > Software Engineering Research Group
    School of Computing and Engineering
    School of Computing and Engineering > Pedagogical Research Group
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    Depositing User: Ahmad Klaib
    Date Deposited: 08 Mar 2011 13:52
    Last Modified: 08 Mar 2011 13:52
    URI: http://eprints.hud.ac.uk/id/eprint/9753

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