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

Dykeman, E.C.

Nucleic Acids Research 43(12): 5708-5715

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, unlike KINFOLD, the KFOLD algorithm utilizes the fact that many of the base-pair addition/deletion reactions and their corresponding rates do not change between each step in the algorithm. This allows KFOLD to achieve a substantial speed-up in the time required to compute a prediction of the folding pathway and, for a fixed number of base-pair moves, performs logarithmically with sequence size. This increase in speed opens up the possibility of studying the kinetics of much longer RNA sequences at single base-pair resolution while also allowing for the RNA folding statistics of smaller RNA sequences to be computed much more quickly.

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