A novel genetic approach for optimized biological sequence alignment


Biological sequence alignment is one of the most important problems in computational biology. The objective of the alignment process is to maximize the alignment score between two given sequences of varying or equal length. The alignment score of two sequences is calculated based on matches, mismatches and gaps in the alignment. We have proposed a new genetic approach for finding optimized match between two DNA or protein sequences. The process is compared with two well known relevant sequence alignment techniques.

Share and Cite:

Garai, G. and Chowdhury, B. (2012) A novel genetic approach for optimized biological sequence alignment. Journal of Biophysical Chemistry, 3, 201-205. doi: 10.4236/jbpc.2012.32022.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Carroll, S.B., Grenier, J.K. and Weatherbee, S.D. (2001) From DNA to diversity: Molecular genetics and the evolutionary of animal designs. Blackwell Science, Malden.
[2] Graur, D. and Li, W.H., (2000) Fundamental of Molecular Evolution. 2nd Edition, Sinauer Associates, Sunderland.
[3] Xiong, J. (2006) Essential Bioinformatics. Cambridge University Press, Cambridge.
[4] Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. Journal of Molecular Biology, 147, 195-197. doi:10.1016/0022-2836(81)90087-5
[5] Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48, 443-453. doi:10.1016/0022-2836(70)90057-4
[6] Othman, M.B., Cherif, A.H. and Azim, G.A. (2008) Genetic algorithms and scalar product for pairwise sequence alignment. International Journal of Computers, 2, pp. 134-147.
[7] Taneda, A., (2010) Multi-objective pairwise RNA sequence alignment. Oxford Journals, Bioinformatics, 26, 2383-2390. doi:10.1093/bioinformatics/btq439
[8] Pond, S.L.K., Posada, D., Gravenor, M.B., Woelk, C.H. and Frost, S.D.W., (2006) GARD: a genetic algorithm for recombination detection. Oxford Journals, Bioinformatics, 22, 3096-3098. doi:10.1093/bioinformatics/btl474
[9] Notredame, C., O’Brien E.A. and Higgins, D.G. (1997) RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Research, 25, 4570-4580. doi:10.1093/nar/25.22.4570
[10] Batzoglou, S. (2005) The many faces of sequence alignment. Briefings in Bioinformatics, 6, 6-22. doi:10.1093/bib/6.1.6

Copyright © 2023 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.