Research ArticleOpen AccessGoogle Scholar indexed
A novel genetic approach for optimized biological sequence alignment
Department of Computational Biology, Saha Institute of Nuclear Physics, Kolkata, India
Department of Bioinformatics, DOEACC Society, Kolkata, India
- 1 Department of Computational Biology, Saha Institute of Nuclear Physics, Kolkata, India
- 2 Department of Bioinformatics, DOEACC Society, Kolkata, India
Journal of Biophysical Chemistry·Volume 03 (2012)·Pages 201–205·Published 29 May 2012·DOI10.4236/jbpc.2012.32022
Copy link · social · email
Abstract
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.
KeywordsSequence AlignmentDNAProteinGenetic AlgorithmComputational Biology
- 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.
- Graur, D. and Li, W.H., (2000) Fundamental of Molecular Evolution. 2nd Edition, Sinauer Associates, Sunderland.
- Xiong, J. (2006) Essential Bioinformatics. Cambridge University Press, Cambridge.
- 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
- 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
- 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.
- Taneda, A., (2010) Multi-objective pairwise RNA sequence alignment. Oxford Journals, Bioinformatics, 26, 2383-2390. doi:10.1093/bioinformatics/btq439
- 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
- 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
- Batzoglou, S. (2005) The many faces of sequence alignment. Briefings in Bioinformatics, 6, 6-22. doi:10.1093/bib/6.1.6