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Erschienen in:
2006 | OriginalPaper | Buchkapitel
Aligning Multiple Protein Sequences by Hybrid Clonal Selection Algorithm with Insert-Remove-Gaps and BlockShuffling Operators
verfasst von : V. Cutello, D. Lee, G. Nicosia, M. Pavone, I. Prizzi
Erschienen in: Artificial Immune Systems
Verlag: Springer Berlin Heidelberg
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Multiple sequence alignment (MSA) is one of the most important tasks in biological sequence analysis. This paper will primarily focus on on protein alignments, but most of the discussion and methodology also applies to DNA alignments. A novel hybrid clonal selection algorihm, called an aligner, is presented. It searches for a set of alignments amongst the population of candidate alignments by optimizing the classical
weighted sum of pairs
objective function. Benchmarks from BaliBASE library (v.1.0 and v.2.0) are used to validate the algorithm. Experimental results of BaliBASE v.1.0 benchmarks show that the proposed algorithm is superior to PRRP, ClustalX, SAGA, DIALIGN, PIMA, MULTIALIGN, and PILEUP8. On BaliBASE v.2.0 benchmarks the algorithm shows interesting results in terms of SP score with respect to established and leading methods, i.e. ClustalW, T-Coffee, MUSCLE, PRALINE, ProbCons, and Spem.