Aligning Multiple Protein Sequences by Hybrid Clonal Selection Algorithm with Insert-Remove-Gaps and BlockShuffling Operators View Full Text


Ontology type: schema:Chapter      Open Access: True


Chapter Info

DATE

2006

AUTHORS

V. Cutello , D. Lee , G. Nicosia , M. Pavone , I. Prizzi

ABSTRACT

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. More... »

PAGES

321-334

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/11823940_25

DOI

http://dx.doi.org/10.1007/11823940_25

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1010010665


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