Abstract—The alignment of biological sequences is a crucial tool in molecular biology and genome analysis. It helps to build a phylogenetic tree of related DNA sequences and also to predict the function and structure of unknown protein sequences by aligning with other sequences whose function and structure is already known. However, finding an optimal multiple sequence alignment takes time and space exponential with the length or number of sequences increases. Genetic Algorithms (GAs) are strategies of random searching that optimize an objective function which is a measure of alignment quality (distance) and has the ability for exploratory search through the solution space and exploitation of current results. In this paper, we view the multiple sequence alignment problems as an optimization problem and present a stochastic approach based on GAs for finding globally optimal multiple alignments in reasonable time, starting from completely unaligned sequences.
Index Terms—Multiple Sequence, Optimization, Genetic Algorithm
Segun. A. Fatumo is a lecturer in the department of Computer and Information Sciences, Covenant University, Ota, Nigeria where he also received his Ph.D. His current research interests are metabolic network modeling and analysis, Drug target identification and validation. He is a member of many internationally recognized professional societies. He was the founder and pioneer president of Region Student Group of International Society of Computational Biology-Student Council (ISCB-SC).
Ibidapo O. Akinyemi is a Ph.D. student in the Department of Computer and Information Sciences, Covenant University, Ota, Nigeria. He holds B. Sc. Mathematical Sciences (Computer Science option) and M. Sc. (Computer Science) . His current research interests are on Computational Intelligence and Software Engineering. He is a member of the Nigeria Computer Society and Computer Professional Registration Council of Nigeria.
Ezekiel F. Adebiyi is a Senior Lecturer and the group leader of the Bioinformatics unit of the Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria. He received his Ph.D. in Algorithm and Bioinformatics from the University of Tuebingen
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Cite: Segun A. Fatumo, Ibidapo O. Akinyemi and Ezekiel .F. Adebiyi, "Aligning Multiple Sequences with Genetic Algorithm,"
International Journal of Computer Theory and Engineering vol. 1, no. 2, pp. 179-182, 2009.
