Ensemble-based RNA secondary structure characterization (Engineering in Genomics)

Free energy minimization methods of predicting RNA secondary structure have proven valuable to the interpretation of experimental data but suffer from the inability to meaningfully address the ensemble of structures expected by statistical thermodynamic principles. Methods to address the ensemble have been developed but rely on visual inspection or suboptimal clustering techniques. This restricts the usefulness of these methods in automated in silico experiments. A recent statistical algorithm allows the generation of a large ensemble of secondary structures on a given sequence that samples the Boltzmann distribution of such structures.