Approximation Algorithm and Scheme for RNA Maximum Weighted Stacking

Pseudoknotted RNA structure prediction is an important problem in bioinformatics. Existing polynomial time algorithms have no performance guarantee or can handle only limited types of pseudoknots. In this paper for the general problem of pseudoknotted RNA structure prediction, maximum weighted stacking problem is presented based on stacking actions, and its polynomial time approximation algorithm with O(nlogn) time and O(n) space and polynomial time approximation scheme are given. The approximate performance ratio of this approximation algorithm is 3. Compared with existing polynomial time algorithm, they have exact approximation performance and can predict arbitrary pseudoknots.