Abstract
Secondary structure prediction (with or without pseudoknots) of an RNA molecule is a well-known problem in computational biology. Most of the existing algorithms have an assumption that each nucleotide can interact with at most one other nucleotide. This assumption is not valid for triple helix structure (a pseudoknotted structure with tertiary interactions). As these structures are found to be important in many biological processes, it is desirable to develop a prediction tool for these structures. We provide the first structural prediction algorithm to handle triple helix structures. Our algorithm runs in O(n 3) time where n is the length of input RNA sequence. The accuracy of the prediction is reasonably high, with average sensitivity and specificity over 80% for base pairs, and over 70% for tertiary interactions.