Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set
We presented here an algorithm that, given a combinatorial set and parameter k, predicts the k secondary structures with lowest minimum free energies in the combinatorial set. When the number of words in each set of the overall input-set is considered to be a constant, our algorithm runs in O(skn3) time. In our algorithms, given a combination C, we look at the minimum free energy structure only. Extensions of these problems would be to find suboptimal structures (i.e. whose free energy is greater than the MFE), or to consider pseudoknots. Another problem for future work would be to find an algorithm with better running time, for example O(n3 + k).
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