A dynamic programming algorithm for RNA structure prediction including pseudoknots.

@article{Rivas1999ADP,
  title={A dynamic programming algorithm for RNA structure prediction including pseudoknots.},
  author={Elena Rivas and Sean R. Eddy},
  journal={Journal of molecular biology},
  year={1999},
  volume={285 5},
  pages={
          2053-68
        }
}
  • E. Rivas, S. Eddy
  • Published 27 July 1998
  • Computer Science, Physics, Biology, Medicine
  • Journal of molecular biology
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 present an implementation of the algorithm that generates the optimal minimum energy structure for a single RNA sequence, using standard RNA… Expand

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