Sciweavers

Share
CPM
2008
Springer

Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots

8 years 4 months ago
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
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.
Mathias Möhl, Sebastian Will, Rolf Backofen
Added 19 Oct 2010
Updated 19 Oct 2010
Type Conference
Year 2008
Where CPM
Authors Mathias Möhl, Sebastian Will, Rolf Backofen
Comments (0)
books