Branch-and-cut algorithm for multiple sequence alignment

K. Reinert, H. P. Lenhof, P. Mutzel, K. Mehlhorn, John D Kececioglu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

42 Citations (Scopus)

Abstract

Multiple sequence alignment is an important problem in computational biology. We study the Maximum Trace formulation introduced by Kececioglu [Kec91]. We first phrase the problem in terms of forbidden subgraphs, which enables us to express Maximum Trace as an integer linear-programming problem, and then solve the integer linear program using methods from polyhedral combinatorics. The trace polytope is the convex hull of all feasible solutions to the Maximum Trace problem; for the case of two sequences, we give a complete characterization of this polytope. This yields a polynomial-time algorithm for a general version of pairwise sequence alignment that, perhaps suprisingly, does not use dynamic programming; this yields, for instance, a non-dynamic-programming algorithm for sequence comparison under the 0-1 metric, which gives another answer to a long-open question in the area of string algorithms [PW93]. For the multiple-sequence case, we derive several classes of facet-defining inequalities and show that for all but one class, the corresponding separation problem can be solved in polynomial time. This leads to a branch-and-cut algorithm for multiple sequence alignment, and we report on our first computational experience. It appears that a polyhedral approach to multiple sequence alignment can solve instances that are beyond present dynamic-programming approaches.

Original languageEnglish (US)
Title of host publicationProceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB
PublisherACM
Pages241-250
Number of pages10
StatePublished - 1997
Externally publishedYes
EventProceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB - Santa Fe, NM, USA
Duration: Jan 20 1997Jan 23 1997

Other

OtherProceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB
CitySanta Fe, NM, USA
Period1/20/971/23/97

Fingerprint

Dynamic programming
Polynomials
Linear programming

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Reinert, K., Lenhof, H. P., Mutzel, P., Mehlhorn, K., & Kececioglu, J. D. (1997). Branch-and-cut algorithm for multiple sequence alignment. In Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB (pp. 241-250). ACM.

Branch-and-cut algorithm for multiple sequence alignment. / Reinert, K.; Lenhof, H. P.; Mutzel, P.; Mehlhorn, K.; Kececioglu, John D.

Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB. ACM, 1997. p. 241-250.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Reinert, K, Lenhof, HP, Mutzel, P, Mehlhorn, K & Kececioglu, JD 1997, Branch-and-cut algorithm for multiple sequence alignment. in Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB. ACM, pp. 241-250, Proceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB, Santa Fe, NM, USA, 1/20/97.
Reinert K, Lenhof HP, Mutzel P, Mehlhorn K, Kececioglu JD. Branch-and-cut algorithm for multiple sequence alignment. In Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB. ACM. 1997. p. 241-250
Reinert, K. ; Lenhof, H. P. ; Mutzel, P. ; Mehlhorn, K. ; Kececioglu, John D. / Branch-and-cut algorithm for multiple sequence alignment. Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB. ACM, 1997. pp. 241-250
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