Abstract
Secondary structure prediction of an RNA molecule is an important but challenging computational problem, in particular when the structure contains pseudoknots. Most existing algorithms target at restricted pseudoknot structures. However, all these algorithms have an assumption that each nucleotide can interact with at most one nucleotide. This assumption is not valid for triple helix structure (a pseudoknotted structure with tertiary in- teraction). In this thesis, we provide the rst structural prediction solution to handle these tertiary interactions. Our algorithm runs in O(n3) time. The accuracy of the prediction is reasonably high, with average sensitivity and speci city over 80% for base pairs, and over 70% for tertiary interactions.