Sciweavers

Share
WABI
2010
Springer

Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs

10 years 1 months ago
Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs
Abstract. We present three heuristic strategies for folding RNA sequences into secondary structures including kissing hairpin motifs. The new idea is to construct a kissing hairpin motif from an overlay of two simple canonical pseudoknots. The difficulty is that the overlay does not satisfy Bellman’s Principle of Optimality, and the kissing hairpin cannot simply be built from optimal pseudoknots. Our strategies have time/space complexities of O(n4 )/O(n2 ), O(n4 )/O(n3 ), and O(n5 )/O(n2 ). All strategies have been implemented in the program pKiss and were evaluated against known structures. Surprisingly, our simplest strategy performs best. As it has the same complexity as the previous algorithm for simple pseudoknots, the overlay idea opens a way to construct a variety of practically useful algorithms for pseudoknots of higher topological complexity within O(n4 ) time and O(n2 ) space.
Corinna Theis, Stefan Janssen, Robert Giegerich
Added 31 Jan 2011
Updated 31 Jan 2011
Type Journal
Year 2010
Where WABI
Authors Corinna Theis, Stefan Janssen, Robert Giegerich
Comments (0)
books