The biomedical importance of small RNA molecules continues to grow. Yet, even at this length scale, reliably predicting the native base pairs remains a significant open problem. The ability to sample secondary structures efficiently from the Gibbs distribution yields a strong signal of high probability pairings. However, further analysis is needed to identify important correlations in these large data sets. RNA profiling is a new method which identifies the most probable combinations of base pairs across the ensemble of possible secondary structures.