An implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update
نویسندگان
چکیده
منابع مشابه
An implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update
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 c...
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15 صفحه اولRNA folding kinetics using Monte Carlo and Gillespie algorithms.
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can ...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2015
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkv480