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Multiple Sequence Alignment with Multiobjective Metaheuristics. A Comparative Study
Author(s) -
ZambranoVega Cristian,
Nebro Antonio J.,
Durillo Juan J.,
GarcíaNieto José,
AldanaMontes José F.
Publication year - 2017
Publication title -
international journal of intelligent systems
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.291
H-Index - 87
eISSN - 1098-111X
pISSN - 0884-8173
DOI - 10.1002/int.21892
Subject(s) - metaheuristic , sequence (biology) , computer science , artificial intelligence , data mining , biology , genetics
Multiple sequence alignment (MSA) plays a core role in most bioinformatics studies and provides a framework for the analysis of evolution in biological systems. The MSA problem consists in finding an optimal alignment of three or more sequences of nucleotides or amino acids. Different scores have been defined to assess the quality of MSA solutions, so the problem can be formulated as a multiobjective optimization problem. The number of proposals focused on this approach in the literature is scarce, and most of the works take as base algorithm the NSGA‐II metaheuristic. So, there is a lack of a study involving a set of representative multiobjective metaheuristics to deal with this complex problem. Our main goal in this paper is to carry out such study. We propose a biobjective formulation for the MSA and perform an exhaustive comparative study of six multiobjective algorithms. We have considered a number of problems taken from the benchmark BAliBASE (v3.0). Our experiments reveal that the classic NSGA‐II algorithm and MOCell, a cellular metaheuristic, provide the best overall performance.