Operational Research in Engineering Sciences

Journal DOI: https://doi.org/10.31181/oresta190101s

(A Journal of Management and Engineering) ISSN 2620-1607 | ISSN 2620-1747 |

COMPARATIVE ANALYSIS OF BIT-PARALLEL STRING PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES

Muhammad Yusuf Muhammad ,
American University of Nigeria, PMB 2250 Yola, Adamawa State, Nigeria
Mathias Fonkam ,
American University of Nigeria, PMB 2250 Yola, Adamawa State, Nigeria
Salu George Thandekatu ,
American University of Nigeria, PMB 2250 Yola, Adamawa State, Nigeria
Sandip Rakshit ,
American University of Nigeria, PMB 2250 Yola, Adamawa State, Nigeria
Rao Narasimha Vajjhala ,
American University of Nigeria, PMB 2250 Yola, Adamawa State, Nigeria

Abstract

The inherent parallelism in a bit operation like AND/OR inside a computer word is known as bit parallelism. It plays a greater role in string pattern matching and has good application in the analysis of biological data. The use of recently developed bit parallel string matching algorithms approaches helps in improving the efficiency of the other string pattern matching algorithms. This paper discusses the working of some of these bit parallel string matching algorithms and their application on biological sequences. It also shows how bit-parallelism can be efficiently used to address various matching problems in Bioinformatics to analyze biological sequences such as Deoxyribonucleic acid (DNA), Ribonucleic acid (RNA), and Protein with examples. It can also serve as a greater tool for researchers when looking for the appropriate method to use on Biological sequences.

Keywords
Bit-parallelism, Automaton, Pattern matching, Ribonucleic acid, Parameterized matching.

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CiteScore for Management Science and Operations Research

8.1
2021CiteScore
 
 
89th percentile
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CiteScore for Engineering (miscellaneous)

8.1
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93rd percentile
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