Publication details

Saarland University Computer Science

Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots

Mathias Möhl, Sebastian Will, Rolf Backofen

Proceedings of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM 2008), 2008

We present an algorithm that computes 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 \etal~\citeJiang2002 to arbitrary pseudoknots. In their absence, it gracefully degrades to the same polynomial algorithm. A prototypical implementation demonstrates the applicability of the method.

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