Browse > Article

An Efficient Method for Multiple Sequence Alignment using Subalignment Refinement  

Kim, Jin (한림대학교 정보통신공학부)
Jung, Woo-Cheol (한림대학교 컴퓨터공학과)
Uhmn, Saang-Yong (한림대학교 교양교육부)
Publication Information
Journal of KIISE:Software and Applications / v.30, no.9, 2003 , pp. 803-811 More about this Journal
Abstract
Multiple sequence alignment is a useful tool to identify the relationships among protein sequences. Dynamic programming is the most widely used algorithm to obtain multiple sequence alignment with optimal cost. However, dynamic programming cannot be applied to certain cost function due to its drawback and cannot be used to produce optimal multiple sequence alignment. We propose sub-alignment refinement algorithm to overcome the problem of dynamic programming. Also we show proposed algorithm can solve the problem of dynamic programming efficiently.
Keywords
multiple sequence alignment; optimization algorithm; dynamic programming;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Altschul, S. F. and Lipman, D. J. 'Threes, stars, and multiple biological sequence alignment,' SIMA J. appl. Math, Vol.49 pp.197-209, 1989   DOI   ScienceOn
2 Kim, J. and Pramanik, S. and M. J. Chung, 'Multiple sequence alignment using simulated annealing,' CABIOS, Vol.10, pp.419-426, 1994   DOI   ScienceOn
3 Kim, J. and Pramanik, S. 'An effecient method for multiple seqence alignment,' In Second International Conference on Intelligent Systems for Molecular Biology, 1994
4 Murata, M., Richardson, J. S., and Sussman, J. L. 'Simultaneous comparison of three protein sequences,' In Proc. Natil. Acad. Sci. U.S.A., Vol.82, pp.3073-3077, 1985   DOI
5 Altschul, S. F. 'Gap costs for multiple sequence alignment,' J. Theor. Biol., Vol.138 pp.297-309. 1989   DOI
6 Lipman, D. J., Altschul, S. F. and Kececioglu, J. D. 'A tool for multiple sequence alignment,' Proc. Natl. Acad. Sci. U.S.A., Vol.86, pp. 4412-4415, 1989   DOI
7 Martinez, H. M. 'A flexible multiple sequence alignment program,' Nucl. Acids. Res., Vol16, pp.1683-1691, 1988   DOI
8 Dayhoff, M. O. 'A model of evolutionary change in proteins. matrices for detecting distance relationships,' In Atlas of Protein sequence on Structure, Vol. 5, suppl.3, pp.354-352. Dayhoff, M. O.(ed.) Washington. DC: National Biomedical Research Foundation, 1978
9 Ficket, J. W. 'Fast optimal alignment,' Nucl. Acids Res., Vol.12 pp.175-180, 1984   DOI
10 Needleman, S.B and Wunch, C. D. 'A general method applicable to the serch for similarities in the amino acid sequence of two proteins,' J. Molec. Biol., Vol. 48, pp. 443-453, 1970   DOI
11 Chen, S. C. C., Wong, A. K., and Chiu, D. K. Y. 'A survey of multiple sequence comparison methods,' Bull. Math. Bio., Vol.43, pp.563-598, 1992   DOI
12 Feng, D. F., Johnson, M. S., and Doolittle, R. F. 'Aligning amino acid sequences: comparison of commonly used methods,' J. Molec. Evol., Vol.21, pp. 112-125, 1982   DOI
13 Sankoff, D. and Kruskal, J. B. 'Time Warps, String Edits and macromolecules: The theory and practice of Sequence Comparison,' Addison Wesley, Reading, MA, 1983
14 Feng, D. F. and Doolittle, R. F. 'Progressive sequence alignment as a prerequisite to correct phylogenetic trees,' J. Molec. Evol., 25:351-360, 1987   DOI
15 Notredame, C. and Higgins, D. 'SAGA:sequence alignment by genetic algorithm,' Nucl. Acids. Res., Vol.24, No.8, pp.1515-1524, 1996   DOI
16 Sankoff, D. 'Simultaneous comparison of three or more sequence related by a tree,' Addison Wesley, Reading, MA, 1983
17 Smith, T. F and Waterman, M. S. 'Identification of common molecular subsequence,' J. Mol. Biol. Vol. 147, pp.195-197, 1981   DOI
18 Taylor, W. R. 'Multiple sequence alignment by a pairwise algorithm,' CABIOS, Vol.3, pp.81-87, 1987