Fast Folding and Comparison of RNA Secondary Structures

Computer codes for computation and comparison of RNA secondary structures, the {\tt Vienna RNA package}, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities. <p> An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment. All computer codes are written in {\tt ANSI C}. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.