On the parallel prediction of the RNA secondary structure

We present the parallelization of the Vienna Package algorithm that predicts the secondary structure of the RNA. Before the tool can be effectively used it must be tuned on the target architecture. This tune consist of finding the the sizes for optimal executions. We have developed an analytical model to find these optimal the sizes. The validity of the analytical model developed for the parallel algorithms presented in [1] is studied through an extensive set of experiments performed on a Origin 3000. We present a statistical model, to deal with the cases where the hypothesis of the analytical model are not satisfied. The algorithms are satisfactorily applied to real sequences.