Comparison of dynamic programming and evolutionary algorithms for RNA secondary structure prediction

This paper builds on previous research from an EA used to predict secondary structure of RNA molecules. The EA has the goal of predicting which canonical base pairs will form hydrogen bonds and helices. The addition of stacking energies, through INN and INN-HB, to our thermodynamic model has enhanced our predictions. In this paper, we test three RNA sequences of lengths 118, 543, and 784 nucleotides using a variety of previously successful operators and parameter settings. The accuracy of the predicted structures are compared against those generated by the Nussinov DPA and also to known structures. The EA showed high accuracy of prediction especially on short sequences. On all tested sequences, the EA outperforms the Nussinov DPA.