An RNA Pseudoknot Folding Algorithm Based on Heuristic Searching

The general problem for the prediction of RNA secondary structure with pseudoknots is NP-hard. For a restricted class of pseudoknots, it was traditionally solved by the dynamic programming approach. However, these algorithms are computationally very expensive, when the input sequence or the contained pseudoknot is too long. We present a heuristic algorithm for RNA secondary structures with pseudoknots prediction. We shall point out that the problem can be considered as a tree searching problems and can be solved by our algorithm effectively. It is very efficient and can be used as a practical tool especially for pseudoknots.