### 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 language | English (US) |
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Title of host publication | Combinatorial Pattern Matching - 4th Annual Symposium, CPM 1993, Proceedings |

Editors | Alberto Apostolico, Alberto Apostolico, Maxime Crochemore , Zvi Galil, Zvi Galil, Udi Manber |

Publisher | Springer-Verlag |

Pages | 106-119 |

Number of pages | 14 |

ISBN (Print) | 9783540567646 |

DOIs | |

State | Published - 1993 |

Externally published | Yes |

Event | Conference 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 2017 → Sep 15 2017 |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 684 LNCS |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Conference

Conference | Conference of the European Society for Fuzzy Logic and Technology, EUSFLAT 2017 and 16th International Workshop on Intuitionistic Fuzzy Sets and Generalized Nets, IWIFSGN 2017 |
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Country | Poland |

City | Warsaw |

Period | 9/11/17 → 9/15/17 |

### ASJC Scopus subject areas

- Theoretical Computer Science
- Computer Science(all)

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## Cite this

*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