An algorithm and a computer program have been prepared for determining RNA secondary structures within any prescribed increment of the computed global minimum free energy. The mathematical problem of determining how weU d e h e d a minimum energy folding is can now be solved. AU predicted base pairs that can participate i n subophal strucrures may be displayed and analyzed graphically. Representative suboptimal foldings are generated by selecting these base pairs one at a time and computing the

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... best fordings that contain them. A distance criterion that ensures that no two structures are ' ( t o o close" is used to avoid multiple generation of similar structures. Thermodynamic parameters, including fieeenergy increments for single-base stacking at the ends of helices and for terminal mismatched pairs in interior and hairpin loops, are incorporated into the underlying folding model of the above algorithm.