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.
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Möhl, M., Will, S., Backofen, R. (2008). Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. In: Ferragina, P., Landau, G.M. (eds) Combinatorial Pattern Matching. CPM 2008. Lecture Notes in Computer Science, vol 5029. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69068-9_9
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DOI: https://doi.org/10.1007/978-3-540-69068-9_9
Publisher Name: Springer, Berlin, Heidelberg
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