Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree

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

6 Scopus citations

Abstract

We consider the problem of aligning sequences related by a given evolutionary tree: given a fixed tree with its leaves labeled with sequences, find ancestral sequences to label the internal nodes so as to minimize the total cost of all the edges in the tree. The cost of an edge is the edit distance between the sequences labeling its endpoints. In this paper, we consider the case when the given tree is a regular d-ary tree for some fixed d and provide a d+1/d-1-approximation algorithm for this problem that runs in time O(d(2kn)d+ n2k2d) where k is the number of leaves in the tree and n is the maximum length of any of the sequences labeling the leaves. We also consider a new bottleneck objective in labeling the internal nodes. In this version, we wish to find the labeling of the internal nodes that minimizes the maximum cost of any edge in the tree. For this problem we provide a simple 2δ + 1-approximation algorithm where 8 is the depth of the given undirected tree defined as the maximum over all internal nodes of the number of edges from the internal node to a closest leaf. For phylogenetic trees on n nodes that have no internal nodes of degree two, δ ≤ lg n.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
PublisherSpringer Verlag
Pages330-339
Number of pages10
Volume937
ISBN (Print)3540600442, 9783540600442
DOIs
StatePublished - 1995
Externally publishedYes
Event6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995 - Espoo, Finland
Duration: Jul 5 1995Jul 7 1995

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume937
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other6th Annual Symposium on Combinatorial Pattern Matching, CPM 1995
CountryFinland
CityEspoo
Period7/5/957/7/95

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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  • Cite this

    Ravi, R., & Kececioglu, J. D. (1995). Approximation algorithms for multiple sequence alignment under a fixed evolutionary tree. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 937, pp. 330-339). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 937). Springer Verlag. https://doi.org/10.1007/3-540-60044-2_52