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Seeded Tree Alignment and Planar Tanglegram Layout

  • Antoni Lozano
  • Ron Y. Pinter
  • Oleg Rokhlenko
  • Gabriel Valiente
  • Michal Ziv-Ukelson
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4645)

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.

Keywords

Primary Seed Planar Layout Unordered Tree Secondary Seed Dynamic Programming Table 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Antoni Lozano
    • 1
  • Ron Y. Pinter
    • 2
  • Oleg Rokhlenko
    • 2
  • Gabriel Valiente
    • 3
  • Michal Ziv-Ukelson
    • 4
  1. 1.Logic and Programming Research Group, Technical University of Catalonia, E-08034 BarcelonaSpain
  2. 2.Department of Computer Science, Technion – Israel Institute of Technology, Haifa 32000Israel
  3. 3.Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia, E-08034 BarcelonaSpain
  4. 4.School of Computer Science, Tel-Aviv University, Tel-Aviv 69978Israel

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