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A Novel Approach to Multiple Sequence Alignment Using Multiobjective Evolutionary Algorithm Based on Decomposition
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DOI：10.1109/JBHI.2015.2403397.png)
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摘要
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Multiple sequence alignment (MSA) is a fundamental and key step for implementing other tasks in bioinformatics, such as phylogenetic analyses, identification of conserved motifs and domains, structure prediction, etc. Despite the fact that there are many methods to implement MSA, biologically perfect alignment approaches are not found hitherto. This paper proposes a novel idea to perform MSA, where MSA is treated as a multi-objective optimization problem. A famous multiobjective evolutionary algorithm framework based on decomposition is applied for solving MSA, named MOMSA. In the MOMSA algorithm, we develop a new population initialization method and a novel mutation operator. We compare the performance of MOMSA with several alignment methods based on evolutionary algorithms, including VDGA, GAPAM, and IMSA, and also with state-of-the-art progressive alignment approaches, such as MSAprobs, Probalign, MAFFT, Procons, Clustal omega, T-Coffee, Kalign2, MUSCLE, FSA, Dialign, PRANK, and CLUSTALW. These alignment algorithms are tested on benchmark datasets BAliBASE 2.0 and BAliBASE 3.0. Experimental results show that MOMSA can obtain the significantly better alignments than VDGA, GAPAM on the most of test cases by statistical analyses, produce better alignments than IMSA in terms of TC scores, and also indicate that MOMSA is comparable with the leading progressive alignment approaches in terms of quality of alignments.
Keyword:
Multiobjective evolutionary algorithm framework based on decomposition (MOEA/D)
multiobjective optimization
multiple sequence alignment (MSA)
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6.8
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4.6K
被引数:
2.0W
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引用论文
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmarkBAliBASE 3.0: 多序列比对基准的最新进展
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分享收藏Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega使用Clustal Omega快速，可扩展地生成高质量的蛋白质多序列比对
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OAAI分享收藏分享收藏分享收藏BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.png)
NUCLEIC ACIDS RESEARCH
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NUCLEIC ACIDS RESEARCHIF13.1
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