@techreport{ReinertLenhofMutzelMehlhornKececioglou96,
TITLE = {A branch-and-cut algorithm for multiple sequence alignment},
AUTHOR = {Reinert, Knut and Lenhof, Hans-Peter and Mutzel, Petra and Mehlhorn, Kurt and Kececioglou, John},
LANGUAGE = {eng},
URL = {http://domino.mpi-inf.mpg.de/internet/reports.nsf/NumberView/1996-1-028},
NUMBER = {MPI-I-1996-1-028},
INSTITUTION = {Max-Planck-Institut f{\"u}r Informatik},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {1996},
DATE = {1996},
ABSTRACT = {Multiple sequence alignment is an important problem in computational biology. We study the Maximum Trace formulation introduced by Kececioglu~\cite{Kececioglu91}. 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 {\it 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 \cite{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.},
TYPE = {Research Report / Max-Planck-Institut für Informatik},
}