A new pseudoknots folding algorithm for RNA structure prediction

Abstract

A new dynamic programming algorithm with O(n4) time and O(n 3) space is presented to predict the RNA secondary structure including nested pseudoknots and a subclass of crossed pseudoknots. Compared with the Jens algorithm of O(n4) time and O(n2) space, this algorithm can predict more complex pseudoknots. Compared with the Rivas algorithm of O(n6) time and O(n4) space, this algorithm has the same power for the planar pseudoknots prediction. © Springer-Verlag Berlin Heidelberg 2005.