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Efficient Chaining of Seeds in Ordered Trees

  • Julien Allali
  • Cédric Chauve
  • Pascal Ferraro
  • Anne-Laure Gaillard
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6460)

Abstract

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m 2 log(m)) in time and O(m 2) in space.

Keywords

Time Complexity Maximum Chain Order Tree Valid Mapping Border Node 
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 2011

Authors and Affiliations

  • Julien Allali
    • 1
    • 2
    • 3
  • Cédric Chauve
    • 3
  • Pascal Ferraro
    • 1
    • 2
    • 4
  • Anne-Laure Gaillard
    • 1
  1. 1.LaBRIUniversité Bordeaux 1, IPB, CNRSFrance
  2. 2.Pacific Institute for Mathematical Sciences and CNRS UMI3069France
  3. 3.Department of MathematicsSimon Fraser UniversityCanada
  4. 4.Department of Computer ScienceUniversity of CalgaryCanada

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