McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots

@inproceedings{Bon2013McGenusAM,
  title={McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots},
  author={Micha{\"e}l Bon and Cristian Micheletti and Henri Orland},
  booktitle={Nucleic acids research},
  year={2013}
}
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and performs an advanced stochastic search of their minimum free energy structure allowing for non-trivial pseudoknot topologies. Specifically, McGenus uses a Monte Carlo algorithm with replica exchange for minimizing a general scoring function which includes not only… CONTINUE READING
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