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 4 ) time exact algorithm and an O(n 4− ) 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. ?
The algorithm had O (n^4) complexity, and was based on base-pair maximization REF .
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Discrete Applied Mathematics
Computer Science Mathematics