Folding 3-noncrossing RNA pseudoknot structures

Simple item page
dc.creatorHuang, Fenix W. D.
dc.creatorPeng, Wade W. J.
dc.creatorReidys, Christian M.
dc.date2008-09-29
dc.date.accessioned2026-07-07T10:06:04Z
dc.date.available2026-07-07T10:06:04Z
dc.descriptionIn 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, $σ$-canonical RNA structure. Here an RNA structure is 3-noncrossing if it does not contain more than three mutually crossing arcs and $σ$-canonical, if each of its stacks has size greater or equal than $σ$. 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.
dc.description32pages, 27figures
dc.identifierhttps://arxiv.org/abs/0809.4840
dc.identifierhttp://arxiv.org/abs/0809.4840
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/170202
dc.subjectCombinatorics
dc.subject05B30
dc.titleFolding 3-noncrossing RNA pseudoknot structures
dc.typetext

Files

Collections

arXiv