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RSMA matching algorithm for searching biological sequences

Klaib, Ahmad and Osborne, Hugh (2009) RSMA matching algorithm for searching biological sequences. In: IIT'09 Proceedings of the 6th international conference on Innovations in information technology. IEEE Press, New Jersey USA, pp. 190-194. ISBN 978-1-4244-5698-7

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Abstract

Huge amounts of biological data are stored in linear files. Biological proteins are sequences of amino acids. The quantities of data in these fields tend to increase year on year. String matching algorithms playa key role in many computer science problems, and in the implementation of computer software. For this reason efficient string-matching algorithms should be used which use minimal computer storage and which minimize the searching response time. In this study, we propose a new algorithm called the Random String Matching Algorithm (RSMA). RSMA combines our enhanced preprocessing phase from the Berry Ravindran algorithm with our proposed new searching phase procedure. This variety ofsearching order allows our proposed algorithm to reduce the number of comparison characters and enhances the searching response time. Experimental results show that the RSMA algorithm offers a smaller number of comparisons and offers improved elapsed searching time when compared to other well-known algorithms.

Item Type: Book Chapter
Subjects: Q Science > Q Science (General)
Q Science > QD Chemistry
Schools: School of Computing and Engineering
School of Computing and Engineering > Informatics Research Group > Software Engineering Research Group
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Depositing User: Sara Taylor
Date Deposited: 22 Mar 2011 15:13
Last Modified: 22 Mar 2011 15:13
URI: http://eprints.hud.ac.uk/id/eprint/9922

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