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

Arakil Chentoufi, Abdelhakim El Fatmi, M. A. Bekri, Said Benhlima, M. Sabbane
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引用次数: 0

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.
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基于多目标优化思想的RNA多重比对启发式求解方法
多序列比对(MSA)是生物信息学中一个NP完全的重要问题。出于这个原因,已经开发了许多计算方法来实现最佳对准。然而,这一目标仍然是一个巨大的挑战。MSA也可以看作是一个多目标优化问题。同样,我们提出了一种使用Pareto Front和遗传算法(GA)的新方法,称为MOO-RNA,来排列一组RNA序列。我们在Bralibase II的一组比对上验证了我们的方法。结果表明,我们的方法在对和分数(SPS)和结构守恒指数(SCI)方面的质量得到了提高。
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来源期刊
International Review of Automatic Control
International Review of Automatic Control Engineering-Control and Systems Engineering
CiteScore
2.70
自引率
0.00%
发文量
17
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