An RNA secondary structure prediction algorithm
This algorithm finds all optimal secondary structures of the RNA sequence AAUACUCCGUUGCAGCAU with the following simplified Zuker minimization algorithm. The following initialisation is used:
j + 5 > i => V(i, j) = W(i, j) = ∞
hairpin energy:
h(i, j) = 2 * (i - j + 5)
and stem energy:
s(i, j) = -4, 0, 4 for Watson-Crick bonds, GU, and all other possible pairs respectively.
Multiloops and buldges are ignored to simplify V so that it only has the first two cases.
In the /output folder you can find the filled-in tables W - V , an optimal fold, its bonds, and the corresponding backtrack path.