Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots

This paper shows simple dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. For a basic version of the problem (i.e., maximizing the number of base pairs), this paper presents an O(n) time exact algorithm and an O(n4− ) time approximation algorithm. The latter one outputs, for most RNA sequences, a secondary structure in which the number of base pairs is at least 1− of the optimal, where ; are any constants satisfying 0¡ ; ¡1. Several related results are shown too. ? 2000 Elsevier Science B.V. All rights reserved.