The structure predicted by our algorithm is not very accurate, as in
reality there are many more factors that determine the formation of
secondary structure of RNA. The actual structure may not have the
maximum number of pairs, which made it difficult for us to verify the
correctness of our code.
Some RNA sequences we found on RNA Central do not fold at all, despite
the dynamic programming function providing a valid set of pairs of
bases. We suspect that we will not be able to find simple minimum free
energy secondary structures for these sequences because they may
contain, knots, pseudo-knots, dimerization, hybridization, etc.
Future Work
Extend our current visualization system for RNA molecules with knots.
Enable the user to add multiple RNA molecules in one single canvas
during visualization.
Add step-by-step animation to elaborate in detail how the sequence of
bases folds to form the RNA secondary structure.