An Algorithm for RNA Pseudoknots

TL;DR

This paper introduces a recursive algorithm for calculating the partition function of singly pseudoknotted RNA, extending previous large N formalism, with a computational complexity proportional to the sixth power of RNA length.

Contribution

It develops a detailed, implementable recursive algorithm for RNA pseudoknot partition functions based on large N formalism, improving computational methods in RNA structure prediction.

Findings

Algorithm computes partition function in O(N^6) time.

Provides a self-contained implementation for researchers.

Advances computational RNA pseudoknot analysis.

Abstract

We further develop the large $ N $ 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.