An implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update

@inproceedings{Dykeman2015AnIO,
  title={An implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update},
  author={Eric C. Dykeman},
  booktitle={Nucleic acids research},
  year={2015}
}
In this paper I outline a fast method called KFOLD for implementing the Gillepie algorithm to stochastically sample the folding kinetics of an RNA molecule at single base-pair resolution. In the same fashion as the KINFOLD algorithm, which also uses the Gillespie algorithm to predict folding kinetics, KFOLD stochastically chooses a new RNA secondary structure state that is accessible from the current state by a single base-pair addition/deletion following the Gillespie procedure. However… CONTINUE READING
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