A branch-and-cut algorithm for multiple sequence alignment
- MPI fuer Informatik, Saabruecken (Germany); and others
Multiple sequence alignment is an important problem in computational biology. We study the Maximum Trace formulation introduced by Kececioglu. We first phrase the problem in terms of forbidden subgraphs, which enables us to express Maximum Trace as an integer linear program using methods from polyhedral combinatories. 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. 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. 9 refs., 5 figs.
- Research Organization:
- Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
- OSTI ID:
- 549020
- Report Number(s):
- CONF-970137--
- Country of Publication:
- United States
- Language:
- English
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