Seeded tree alignment and planar tanglegram layout

Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

13 Scopus citations

Abstract

The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. We introduce a constrained form of this problem in which a partial mapping of a set of nodes in one tree to a corresponding set of nodes in the other tree is given, and present efficient algorithms for both ordered and unordered trees. Whereas ordered tree matching based on seeded nodes has applications in pattern matching of RNA structures, unordered tree matching based on seeded nodes has applications in co-speciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which we give a polynomial-time algorithm.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings
PublisherSpringer Verlag
Pages98-110
Number of pages13
ISBN (Print)9783540741251
DOIs
StatePublished - 1 Jan 2007
Externally publishedYes
Event7th International Workshop on Algorithms in Bioinformatics, WABI 2007 - PhiIadelphia, PA, United States
Duration: 8 Sep 20079 Sep 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4645 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference7th International Workshop on Algorithms in Bioinformatics, WABI 2007
Country/TerritoryUnited States
CityPhiIadelphia, PA
Period8/09/079/09/07

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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