title: Local connectivity of neutral networks.
abstract: This paper studies local connectivity of neutral networks of RNA secondary and pseudoknot structures. A neutral network denotes the set of RNA sequences that fold into a particular structure. It is called locally connected, if in the limit of long sequences, the distance of any two of its sequences scales with their distance in the n-cube. One main result of this paper is that lambda(n) = n(-1/2+Delta) is the threshold probability for local connectivity for neutral networks, considered as random subgraphs of n-cubes. Furthermore, we analyze local connectivity for finite sequence length and different alphabets. We show that it is closely related to the existence of specific paths within the neutral network. We put our theoretical results into context with folding algorithms into minimum-free energy RNA secondary and pseudoknot structures. Finally, we relate our structural findings with dynamics by discussing the role of local connectivity in the context of neutral evolution.
authors.affiliation: Center for Combinatorics, Nankai University, Tianjin, 300071, People's Republic of China. duck@santafe.edu
authors.forename: Christian M
authors.initials: CM
authors.lastname: Reidys
mesh_terms: D001483:Base Sequence / Q000235:genetics; D016000:Cluster Analysis; D019143:Evolution, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D009690:Nucleic Acid Conformation; D011336:Probability; D012313:RNA / Q000737:chemistry / Q000648:ultrastructure*; D012016:Reference Values; D013816:Thermodynamics
chemical_list: D012313:RNA