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A Heuristic Method Based on Multi-Objective Optimization Concept for Solving RNA Multiple Alignment

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Multiple sequence alignment (MSA) is an NP-complete and important problem in Bioinformatics. For this reason, a number of computational approaches has 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.
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Bioinformatics; Multiple Sequence Alignment; Secondary Structure; Objective Function; Optimization Multi-Objective

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