A statistical sampling algorithm for RNA secondary structure prediction.

ABSTRACT: An RNA molecule, particularly a long-chain mRNA, may exist as a population of structures. Further more, multiple structures have been demonstrated to play important functional roles. Thus, a representation of the ensemble of probable structures is of interest. We present a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures. The forward step of the algorithm computes the equilibrium partition functions of RNA secondary structures with recent thermodynamic parameters. Using conditional probabilities computed with the partition functions in a recursive sampling process, the backward step of the algorithm quickly generates a statistically representative sample of structures. With cubic run time for the forward step, quadratic run time in

SUBMITTER: Ding Y 

PROVIDER: S-EPMC297010 | biostudies-literature | 2003 Dec

REPOSITORIES: biostudies-literature