title: Sequence-structure relations of pseudoknot RNA.
abstract: BACKGROUND
  The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two mutually crossing bonds (3-noncrossing). These structures are folded by a novel, ab initio prediction algorithm, cross, capable of searching all 3-noncrossing RNA structures. The algorithm outputs the minimum free energy structure.
  
  
  RESULTS
  After giving some background on RNA pseudoknot structures and providing an outline of the folding algorithm being employed, we present in this paper various, statistical results on the mapping from RNA sequences into 3-noncrossing RNA pseudoknot structures. We study properties, like the fraction of pseudoknot structures, the dominant pseudoknot-shapes, neutral walks, neutral neighbors and local connectivity. We then put our results into context of molecular evolution of RNA.
  
  
  CONCLUSIONS
  Our results imply that, in analogy to RNA secondary structures, 3-noncrossing pseudoknot RNA represents a molecular phenotype that is well suited for molecular and in particular neutral evolution. We can conclude that extended, percolating neutral networks of pseudoknot RNA exist.
authors.affiliation: Center for Combinatorics, LPMC-TJKLC, Nankai University, Tianjin 300071, PR China. fenixprotoss@163.com
authors.forename: Fenix W D
authors.initials: FW
authors.lastname: Huang
authors.forename: Linda Y M
authors.initials: LY
authors.lastname: Li
authors.forename: Christian M
authors.initials: CM
authors.lastname: Reidys
mesh_terms: D000465:Algorithms; D009690:Nucleic Acid Conformation; D010641:Phenotype; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D013816:Thermodynamics
chemical_list: D012313:RNA