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OE Matching Algorithm for Searching Biological Sequences

Klaib, Ahmad and Osborne, Hugh (2009) OE Matching Algorithm for Searching Biological Sequences. In: International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09). ISRST, Orlando, Florida, pp. 36-42. ISBN 978-1-60651-009-4

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    Abstract

    String matching algorithms play a key role in many
    computer science problems, and in the implementation of
    computer software. This problem has received, and
    continues to receive a great deal of attention due to
    various applications in text manipulation, information
    retrieval, speech recognition, image and signal
    processing and computational biology. In this study, we
    propose a new algorithm called the Odd and Even
    algorithm (OE). OE combines an enhanced preprocessing
    phase from the Berry Ravindran algorithm with our
    proposed new searching phase procedure. This variety of
    searching order allows our proposed algorithm to reduce
    the number of comparison characters and enhances the
    searching response time. Experimental results show that
    OE algorithm offers a smaller number of comparisons
    and offers improved elapsed searching time when
    compared to other well-known algorithms for searching
    any length of alphabets and patterns. The proposed
    algorithm is applicable to searching protein sequence
    databases as well as any other string searching
    applications.

    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
    Related URLs:
    Depositing User: Sara Taylor
    Date Deposited: 22 Mar 2011 12:22
    Last Modified: 22 Mar 2011 12:30
    URI: http://eprints.hud.ac.uk/id/eprint/9918

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