The maximum weight trace problem in multiple sequence alignment

Research output: Chapter in Book/Report/Conference proceedingConference contribution

86 Scopus citations

Abstract

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.

Original languageEnglish (US)
Title of host publicationCombinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings
EditorsAlberto Apostolico, Alberto Apostolico, Maxime Crochemore , Zvi Galil, Zvi Galil, Udi Manber
PublisherSpringer-Verlag
Pages106-119
Number of pages14
ISBN (Print)9783540567646
DOIs
StatePublished - 1993
Externally publishedYes
EventConference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2017 and 16th International Workshop on Intuitionistic Fuzzy Sets and Generalized Nets, IWIFSGN 2017 - Warsaw, Poland
Duration: Sep 11 2017Sep 15 2017

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume684 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

ConferenceConference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2017 and 16th International Workshop on Intuitionistic Fuzzy Sets and Generalized Nets, IWIFSGN 2017
CountryPoland
CityWarsaw
Period9/11/179/15/17

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Fingerprint Dive into the research topics of 'The maximum weight trace problem in multiple sequence alignment'. Together they form a unique fingerprint.

  • Cite this

    Kececioglu, J. (1993). The maximum weight trace problem in multiple sequence alignment. In A. Apostolico, A. Apostolico, M. Crochemore , Z. Galil, Z. Galil, & U. Manber (Eds.), Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings (pp. 106-119). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 684 LNCS). Springer-Verlag. https://doi.org/10.1007/bfb0029800