Branch-and-cut algorithm for multiple sequence alignment

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

Research output: Contribution to conferencePaperpeer-review

49 Scopus citations


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)
Number of pages10
StatePublished - 1997
EventProceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB - Santa Fe, NM, USA
Duration: Jan 20 1997Jan 23 1997


OtherProceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB
CitySanta Fe, NM, USA

ASJC Scopus subject areas

  • Engineering(all)


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