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DCMOGA: a New Method for Multiple Sequences Alignment Based on the Principle Divide and Conquers and the Multi-Objective Genetic Algorithm

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In this paper, we present a new algorithm to solve multiple alignments of nucleic acid sequences. The presented method is divided in three steps. Firstly, the algorithm separates the common regions between the aligned sequences (conserved regions) from the non-common regions. Consequently, the first step produces two types of sub-sequences. Secondly, the obtained non-common sub-sequences are aligned using a multi-objective genetic algorithm. Thirdly, we concatenate the sub-alignments obtained from the second step and the similar parts obtained from the first step to construct the final alignment. In order to evaluate the performance of the proposed algorithm, a comparative study has been performed using some of the most popular methods for alignment of nucleic acid sequences and the benchmark Bralibase (Benchmark RNA Database). The obtained results illustrate clearly the effectiveness of the proposed algorithm.
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Bioinformatics; RNA Sequence Alignment; Genetic Algorithm; DCMOGA (Distributed Cooperation Model of Multi-Objective Genetic Algorithm)

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