Folding 3-noncrossing RNA pseudoknot structures

TL;DR

This paper introduces 'cross', an ab initio algorithm for folding RNA pseudoknot structures that are 3-noncrossing and σ-canonical, based on a novel energy model and dynamic programming.

Contribution

It presents a new folding algorithm for RNA pseudoknots that efficiently computes minimum free energy structures with specific crossing and stacking constraints.

Findings

Successfully models 3-noncrossing pseudoknot structures

Integrates motif construction, skeleta-tree generation, and dynamic programming

Provides a self-contained, detailed folding methodology

Abstract

In this paper we present a selfcontained analysis and description of the novel {\it ab initio} folding algorithm {\sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $\sigma$-canonical RNA structure. Here an RNA structure is 3-noncrossing if it does not contain more than three mutually crossing arcs and $\sigma$-canonical, if each of its stacks has size greater or equal than $\sigma$. Our notion of mfe-structure is based on a specific concept of pseudoknots and respective loop-based energy parameters. The algorithm decomposes into three parts: the first is the inductive construction of motifs and shadows, the second is the generation of the skeleta-trees rooted in irreducible shadows and the third is the saturation of skeleta via context dependent dynamic programming routines.