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 to produce an optimal multiple sequence alignment. We propose sub-alignment refinement algorithm to overcome this drawback and impelment this algorithm as a module of our MS Windows-based sequence alignment program which also implements other alignment algorithms and supports several sequence file formats.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Needleman, S.B., Wunch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Molec. Biol. 48, 443–453 (1970)
Altschul, F., Lipman, D.J.: Threes, stars, and multiple biological sequence alignment. SIAM J. appl. Math. 49, 197–209 (1989)
Chan, S.C.C., Wong, A.K., Chiu, D.K.Y.: A survey of multiple sequence comparison methods. Bull. Math. Bio. 43, 563–598 (1992)
Feng, D.F., Doolittle, R.F.: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Molec. Evol. 25, 351–360 (1987)
Feng, D.F., Johnson, M.S., Doolittle, R.F.: Aligning amino acid sequences: comparison of commonly used methods. J. Molec. Evol. 21, 112–125 (1982)
Ficket, J.W.: Fast optimal alignment. Nucl. Acids Res. 12, 175–180 (1984)
Kim, J., Pramanik, S.: An efficient method for multiple sequence alignment. In: Proc. Second International Conference on Intelligent Systems for Molecular Biology, pp. 212–217 (1994)
Kim, J., Pramanik, S., Chung, M.J.: Multiple sequence alignment using simulated annealing. CABIOS 10, 419–426 (1994)
Martinez, H.M.: A flexible multiple sequence alignment program. Nucl. Acids. Res. 16, 1683–1691 (1988)
Murata, M., Richardson, J.S., Sussman, J.L.: Simultaneous comparison of three protein sequences. In Proc. Natl. Acad. Sci. USA. 82, 3073–3077 (1985)
Notredame, C., Higgins, D.: SAGA:sequence alignment by genetic algorithm. Nucl. Acids. Res. 24(8), 1515–1524 (1996)
Sankoff, D.: Simultaneous comparison of three or more sequences related by a tree. Addison-Wesley, Reading (1983)
Sankoff, D., Kruskal, J.B.: Time Warps, String Edits and Macromolecules: The theory and practice of Sequence Comparison. Addison-Wesley, Reading (1983)
Taylor, W.R.: Multiple sequence alignment by a pairwise algorithm. CABIOS 3, 81–87 (1987)
Lipman, D.J., Altschul, S.F., Kececioglu, J.D.: A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. USA. 86, 4412–4415 (1989)
Altschul, S.F.: Gap costs for multiple sequence alignment. J Theor. Biol. 138, 297–309 (1989)
Kim, J., Uhmn, S.: An efficient method for multiple sequence alignment using subalignment refinement. In: Proc. METMBS, pp. 126–132 (2003)
Dayhoff, M.O.: A model of evolutionary change in proteins. matrices for detecting distance relationships. In: Dayhoff., M.O. (ed.) Atlas of Protein sequence an Structure, Washington. DC. National Biomedical Research Foundation, vol. 5, suppl.3, pp. 354–352 (1978)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kim, J., Kim, DH., Uhmn, S. (2004). A Useful Method for Multiple Sequence Alignment and Its Implementation. In: Laganá, A., Gavrilova, M.L., Kumar, V., Mun, Y., Tan, C.J.K., Gervasi, O. (eds) Computational Science and Its Applications – ICCSA 2004. ICCSA 2004. Lecture Notes in Computer Science, vol 3043. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24707-4_11
Download citation
DOI: https://doi.org/10.1007/978-3-540-24707-4_11
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-22054-1
Online ISBN: 978-3-540-24707-4
eBook Packages: Springer Book Archive