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  A branch-and-cut algorithm for multiple sequence alignment

Reinert, K., Lenhof, H.-P., Mutzel, P., Mehlhorn, K., & Kececioglou, J.(1996). A branch-and-cut algorithm for multiple sequence alignment (MPI-I-1996-1-028). Saarbrücken: Max-Planck-Institut für Informatik.

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1996-1-028 (Any fulltext), 11KB
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1996-1-028
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Reinert, Knut1, Author           
Lenhof, Hans-Peter1, Author           
Mutzel, Petra1, Author           
Mehlhorn, Kurt1, Author           
Kececioglou, John1, Author           
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1Algorithms and Complexity, MPI for Informatics, Max Planck Society, ou_24019              

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 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.

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Language(s): eng - English
 Dates: 1996
 Publication Status: Issued
 Pages: 15 p.
 Publishing info: Saarbrücken : Max-Planck-Institut für Informatik
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 Identifiers: URI: http://domino.mpi-inf.mpg.de/internet/reports.nsf/NumberView/1996-1-028
Report Nr.: MPI-I-1996-1-028
BibTex Citekey: ReinertLenhofMutzelMehlhornKececioglou96
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Title: Research Report / Max-Planck-Institut für Informatik
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