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The maximum weight trace problem in multiple sequence alignment

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Combinatorial Pattern Matching (CPM 1993)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 684))

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We define a new problem in multiple sequence alignment, called maximum weight trace. The problem formalizes in a natural way the common practice of merging pairwise alignments to form multiple sequence alignments, and contains a version of the minimum sum of pairs alignment problem as a special case.

Informally, the input is a set of pairs of matched characters from the sequences; each pair has an associated weight. The output is a subset of the pairs of maximum total weight that satisfies the following property: there is a multiple alignment that places each pair of characters selected by the subset together in the same column. A set of pairs with this property is called a trace. Intuitively a trace of maximum weight specifies a multiple alignment that agrees as much as possible with the character matches of the input.

We develop a branch and bound algorithm for maximum weight trace. Though the problem is NP-complete, an implementation of the algorithm shows we can solve instances on as many as 6 sequences of length 250 in a few minutes. These are among the largest instances that have been solved to optimality to date for any formulation of multiple sequence alignment.

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Alberto Apostolico Maxime Crochemore Zvi Galil Udi Manber

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© 1993 Springer-Verlag Berlin Heidelberg

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Kececioglu, J. (1993). The maximum weight trace problem in multiple sequence alignment. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds) Combinatorial Pattern Matching. CPM 1993. Lecture Notes in Computer Science, vol 684. Springer, Berlin, Heidelberg.

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  • Print ISBN: 978-3-540-56764-6

  • Online ISBN: 978-3-540-47732-7

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