An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm.

Abstract:

:One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple sequence alignment has been proposed. Two different genetic operators mainly crossover and mutation were defined and implemented with the proposed method in order to know the population evolution and quality of the sequence aligned. The proposed method is assessed with protein benchmark dataset, e.g., BALIBASE, by comparing the obtained results to those obtained with other alignment algorithms, e.g., SAGA, RBT-GA, PRRP, HMMT, SB-PIMA, CLUSTALX, CLUSTAL W, DIALIGN and PILEUP8 etc. Experiments on a wide range of data have shown that the proposed algorithm is much better (it terms of score) than previously proposed algorithms in its ability to achieve high alignment quality.

journal_name

EXCLI J

journal_title

EXCLI journal

authors

Kumar M

doi

10.17179/excli2015-302

subject

Has Abstract

pub_date

2015-12-15 00:00:00

pages

1232-55

issn

1611-2156

pii

Doc1232

journal_volume

14

pub_type

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