A heuristic method based on multi-objective optimization concept for solving RNA multiple alignment

Abstract

Multiple sequence alignment (MSA) is an NP-complete and important problem in Bioinformatics. For this reason, a number of computational approaches have been developed to achieve the optimal alignment. However, this goal remains a big challenge. MSA can be also treated as a multi-objective optimization problem. In the same way, we present a new method using Pareto Front and Genetic Algorithm (GA), called MOO-RNA, to align a set of RNA sequences. We validate our method on a set of alignments of Bralibase II. The results show that the quality of our method, in terms of Sum-of-Pairs Score (SPS) and Structure Conservation Index (SCI), is improved.