Seeded tree alignment and planar tanglegram layout

  • Authors:
  • Antoni Lozano;Ron Y. Pinter;Oleg Rokhlenko;Gabriel Valiente;Michal Ziv-Ukelson

  • Affiliations:
  • Logic and Programming Research Group, Technical University of Catalonia, Barcelona, Spain;Department of Computer Science, Technion - Israel Institute of Technology, Haifa, Israel;Department of Computer Science, Technion - Israel Institute of Technology, Haifa, Israel;Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, Barcelona, Spain;School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel

  • Venue:
  • WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
  • Year:
  • 2007

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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.