Algorithms for the Prediction of Secondary Structures of RNA Macromolecules

In this paper, we tackle the problem of the prediction by energy computation of RNA stable secondary structures. We present, under the Hypothesis of Loops Dependent Energy (HLDE), our dynamic programming algorithm to compute the free energies of the stable secondary structures and our traceback algorithm to predict these structures. We compute the free energies of the stable secondary structures by using a new approach, called m-Multiloop Approach (m-MA), m > 1. This computation is achieved within a time proportional to n and using a memory space proportional to n. The prediction of the stable secondary structures is achieved within a time proportional to n3 ∗ log3(n). Compared to other approaches, the m-MA enables us to improve the estimation of the minimum energetic contributions of the multiloops. And hence, it enables us to improve the estimation of the free energies of the stable secondary structures.