A branch-and-cut algorithm for multiple sequence alignment

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-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 polynomialtime algorithm for a general version of pairwise sequence alignment that, perhaps suprisingly, does not use dynamic programming; this yields, for instance, a nondynamic-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 ...

• Type: Conference
• Year: 1997
• Where: RECOMB
• Authors: Knut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu
• Keywords: Computational Biology, Maximum Trace, Maximum Trace Formulation, Multiple Sequence Alignment, RECOMB 1997