Folding 3-noncrossing RNA pseudoknot structures

Details Folding 3-noncrossing RNA pseudoknot structures Folding 3-noncrossing RNA pseudoknot structures

2008-09-29

arxiv.org/abs/0809.4840v1

Mathematics

Combinatorics

32pages, 27figures

Scientific paper

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.

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