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RECOMB

1997

Springer

1997

Springer

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 ...

Related Content

Added |
08 Aug 2010 |

Updated |
08 Aug 2010 |

Type |
Conference |

Year |
1997 |

Where |
RECOMB |

Authors |
Knut Reinert, Hans-Peter Lenhof, Petra Mutzel, Kurt Mehlhorn, John D. Kececioglu |

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