Computer codes for computation and comparison of RNA secondary structures, the 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.
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
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.
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