RSMA matching algorithm for searching biological sequences

Ahmad Fadel Klaib, Hugh Osborne

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

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.

Original languageEnglish
Title of host publication2009 International Conference on Innovations in Information Technology, IIT '09
Pages195-199
Number of pages5
DOIs
Publication statusPublished - 2009
EventInternational Conference on Innovations in Information Technology - Al-Ain, United Arab Emirates
Duration: 15 Dec 200917 Dec 2009

Conference

ConferenceInternational Conference on Innovations in Information Technology
Abbreviated titleIIT '09
CountryUnited Arab Emirates
CityAl-Ain
Period15/12/0917/12/09

Fingerprint

String searching algorithms
Computer science
Amino acids
Proteins

Cite this

Klaib, A. F., & Osborne, H. (2009). RSMA matching algorithm for searching biological sequences. In 2009 International Conference on Innovations in Information Technology, IIT '09 (pp. 195-199). [5413769] https://doi.org/10.1109/IIT.2009.5413769
Klaib, Ahmad Fadel ; Osborne, Hugh. / RSMA matching algorithm for searching biological sequences. 2009 International Conference on Innovations in Information Technology, IIT '09. 2009. pp. 195-199
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Klaib, AF & Osborne, H 2009, RSMA matching algorithm for searching biological sequences. in 2009 International Conference on Innovations in Information Technology, IIT '09., 5413769, pp. 195-199, International Conference on Innovations in Information Technology, Al-Ain, United Arab Emirates, 15/12/09. https://doi.org/10.1109/IIT.2009.5413769

RSMA matching algorithm for searching biological sequences. / Klaib, Ahmad Fadel; Osborne, Hugh.

2009 International Conference on Innovations in Information Technology, IIT '09. 2009. p. 195-199 5413769.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Klaib AF, Osborne H. RSMA matching algorithm for searching biological sequences. In 2009 International Conference on Innovations in Information Technology, IIT '09. 2009. p. 195-199. 5413769 https://doi.org/10.1109/IIT.2009.5413769