Topology and prediction of RNA pseudoknots

Mathematical Biology and Ecology Seminar
Wednesday, September 28, 2011 - 11:00
1 hour (actually 50 minutes)
Skiles 005
Dept. of Mathematics & Computer Science, University of Southern Denmark
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.