A dynamic programming algorithm for RNA structure prediction including pseudoknots.

Abstract

We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of O(N6) in time and O(N4) in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from quantum field theory. We… (More)

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Cite this paper

@article{Rivas1999ADP, title={A dynamic programming algorithm for RNA structure prediction including pseudoknots.}, author={Ernesto Rivas and Sean R. Eddy}, journal={Journal of molecular biology}, year={1999}, volume={285 5}, pages={2053-68} }