Abstract
In this paper, we study the constrained sequence alignment problem, which is a generalization of the classical sequence alignment problem with the additional constraint that some characters in the alignment must be positioned at the same columns. The problem finds important applications in Bioinformatics. Our major result is an O(ℓn2)-time and O(ℓn)-space algorithm for constructing an optimal constrained alignment of two sequences where n is the length of the longer sequence and ℓ is the length of the constraint. Our algorithm matches the best known time complexity and reduces the best known space complexity by a factor of n for solving the problem. We also apply our technique to design time and space efficient heuristic and approximation algorithm for aligning multiple sequences.
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Tang, C.Y., Lu, C.L., Chang, M.D.T., Tsai, Y.T., Sun, Y.J., Chao, K.M., Chang, J.M., Chiou, Y.H., Wu, C.M., Chang, H.T., Chou, W.I.: Constrained multiple sequence alignment tool development and its application to RNase family alignment. In: Proceedings of the First IEEE Computer Society Bioinformatics Conference, pp. 127–137 (2002)
Gusfield, D.: Efficient methods for multiple sequence alignment with guaranteed error bounds. Bulletin of Mathematical Biology 30, 141–154 (1993)
Gusfield, D.: Algorithms on strings, trees, and sequence. Cambridge University Press, British (1999)
Higgins, D., Sharpe, P.: CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–244 (1988)
Corpet, F.: Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research 16, 10881–10890 (1988)
Chin, F.Y.L., Ho, N.L., Lam, T.W., Wong, W.H., Chan, M.Y.: Efficient constrained multiple sequence alignment with performance guarantee. In: Proceedings of the IEEE Computational Systems Bioinformatics Conference, pp. 337–346 (2003)
Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22(22), 4673–4680 (1994)
Wang, L., Jiang, T.: On the complexity of multiple sequence alignment. Journal of Computational Biology 1, 337–348 (1994)
Pevzner, P.A.: Multiple alignment, communication cost, and graph matching. SIAM Journal on Applied Mathematics 52, 1763–1779 (1992)
Bonizzoni, P., Vedova, G.D.: The complexity of multiple sequence alignment with SP-score that is a metric. Theoretical Computer Science 259, 63–79 (2001)
Needleman, S., Wunsch, C.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Evolution 48, 443–453 (1970)
Bafna, V., Lawler, E.L., Pevzner, P.A.: Approximation algorithms for multiple sequence alignment. Theoretical Computer Science 182, 233–244 (1997)
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© 2005 Springer-Verlag Berlin Heidelberg
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Peng, Z.S., Ting, H.F. (2005). Time and Space Efficient Algorithms for Constrained Sequence Alignment. In: Domaratzki, M., Okhotin, A., Salomaa, K., Yu, S. (eds) Implementation and Application of Automata. CIAA 2004. Lecture Notes in Computer Science, vol 3317. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30500-2_22
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DOI: https://doi.org/10.1007/978-3-540-30500-2_22
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-24318-2
Online ISBN: 978-3-540-30500-2
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