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Statistical and Bayesian approaches to RNA secondary structure prediction

Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA

Reprint requests to: Ye Ding, Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA; e-mail: yding{at}wadsworth.org; fax: (518) 402-4623.

Prediction of RNA secondary structure is a fundamental problem in computational structural biology. For several decades, free energy minimization has been the most popular method for prediction from a single sequence. In recent years, the McCaskill algorithm for computation of partition function and base-pair probabilities has become increasingly appreciated. This paradigm-shifting work has inspired the developments of extended partition function algorithms, statistical sampling and clustering, and application of Bayesian statistical inference. The performance of thermodynamics-based methods is limited by thermodynamic rules and parameters. However, further improvements may come from statistical estimates derived from structural databases for thermodynamics parameters with weak or little experimental data. The Bayesian inference approach appears to be promising in this context.

Keywords: Boltzmann ensemble; partition function; sampling; Bayesian inference; clustering; RNA secondary structure

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