Georgia Institute of Technology College of Sciences

In this talk we present the natural topological classification of RNA structures in terms of irreducible components that are embedable in surfaces of fixed genus. We add to the conventional secondary structures four building blocks of genus one in order to construct certain structures of arbitrarilyhigh genus. A corresponding unambiguous multiple context free grammar provides an efficient dynamic programming approach for energy minimization, partition function, and stochastic sampling. It admits a topology-dependent parametrization of pseudoknot penalties that increases the sensitivity and positive predictive value of predicted base pairs by 10-20% compared to earlier approaches.