Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots

  • Mathias Möhl
  • Sebastian Will
  • Rolf Backofen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5029)


We present an algorithm for computing the edit distance of two RNA structures with arbitrary kinds of pseudoknots. A main benefit of the algorithm is that, despite the problem is NP-hard, the algorithmic complexity adapts to the complexity of the RNA structures. Due to fixed parameter tractability, we can guarantee polynomial run-time for a parameter which is small in practice. Our algorithm can be considered as a generalization of the algorithm of Jiang et al. [1] to arbitrary pseudoknots. In their absence, it gracefully degrades to the same polynomial algorithm. A prototypical implementation demonstrates the applicability of the method.


RNA alignment pseudoknots fixed parameter tractability 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Mathias Möhl
    • 1
  • Sebastian Will
    • 2
  • Rolf Backofen
    • 2
  1. 1.Programming Systems LabSaarland UniversitySaarbrückenGermany
  2. 2.Bioinformatics, Institute of Computer ScienceAlbert-Ludwigs-UniversitätFreiburgGermany

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