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The Prediction of RNA Secondary Structure

In collaboration with Christine Heitsch (Georgia Tech School of Mathematics) and David Bader (Georgia Tech College of Computing), we are developing methods for predicting RNA secondary structures, combining experimental information with conventional thermodynamic methods.

Our implementation of thermodynamic prediction of RNA secondary structure based on the nearest-neighbor model is GTFold. This fast, scalable multicore program is one to two orders of magnitude faster than conventional folding programs, enabling us to incorporate a number of significant modifications aimed at improving the accuracy of the predictions.