An Algorithm for RNA Pseudoknots
arXiv:cond-mat/0310505
Abstract
We further develop the large formalism presented by some of us in earlier works in order to recursively calculate the partition function of a singly pseudoknotted RNA. We demonstrate that this calculation takes time proportional to the sixth power of the length of the RNA. The algorithm itself is presented in a self-contained form for the convenience of readers interested in implementing it.
21 pages, 14 figures