FAST FOLDING AND COMPARISON OF RNA SECONDARY STRUCTURES

Computer codes for computation and comparison of RNA secondary structu res, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minim um free energies as well as at computations of the equilibrium partiti on functions and base pairing probabilities. An efficient heuristic fo r the inverse folding problem of RNA is introduced. In addition we pre sent compact and efficient programs for the comparison of RNA secondar y structures based on tree editing and alignment. All computer codes a re written in ANSI C. They include implementations of modified algorit hms on parallel computers with distributed memory. Performance analysi s carried out on an Intel Hypercube shows that parallel computing beco mes gradually more and more efficient the longer the sequences are.