Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots

Authors:
Mathias Möhl;Sebastian Will;Rolf Backofen
Affiliations:
Programming Systems Lab, Saarland University, Saarbrücken, Germany;Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany;Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany
Venue:
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Year:
2008

Citing 6
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Abstract

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.