Multiple sequence alignment with affine gap by using multi-objective genetic algorithm

Multiple sequence alignment is of central importance to bioinformatics and computational biology. Although a large number of algorithms for computing a multiple sequence alignment have been designed, the efficient computation of highly accurate and statistically significant multiple alignments is still a challenge. In this paper, we propose an efficient method by using multi-objective genetic algorithm (MSAGMOGA) to discover optimal alignments with affine gap in multiple sequence data. The main advantage of our approach is that a large number of tradeoff (i.e., non-dominated) alignments can be obtained by a single run with respect to conflicting objectives: affine gap penalty minimization and similarity and support maximization. To the best of our knowledge, this is the first effort with three objectives in this direction. The proposed method can be applied to any data set with a sequential character. Furthermore, it allows any choice of similarity measures for finding alignments. By analyzing the obtained optimal alignments, the decision maker can understand the tradeoff between the objectives. We compared our method with the three well-known multiple sequence alignment methods, MUSCLE, SAGA and MSA-GA. As the first of them is a progressive method, and the other two are based on evolutionary algorithms. Experiments on the BAliBASE 2.0 database were conducted and the results confirm that MSAGMOGA obtains the results with better accuracy statistical significance compared with the three well-known methods in aligning multiple sequence alignment with affine gap. The proposed method also finds solutions faster than the other evolutionary approaches mentioned above.