Analysis of RNA sequence structure maps by exhaustive enumeration .1. Neutral networks

Grüner W, Giegerich R, Strothmann D, et al. Analysis of RNA sequence structure maps by exhaustive enumeration .1. Neutral networks. Monatshefte für Chemie. 1996;127(4):355-374.Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that of neutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of(minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms of Zipf's law)