Dynamic programming algorithms for RNA structure prediction with binding sites.

Noncoding antisense RNAs have recently occupied considerable attention and several computational studies have been made on RNA-RNA interaction prediction. In this paper, we present novel dynamic programming algorithms for predicting the minimum energy secondary structure when binding sites of one of the two interacting RNAs are known. Experimental results on several known RNA-RNA interaction data show that our proposed method achieves good performance in accuracy and time.