ANALYSIS OF RNA SEQUENCE STRUCTURE MAPS BY EXHAUSTIVE ENUMERATION .2.STRUCTURES OF NEUTRAL NETWORKS AND SHAPE SPACE COVERING

The relations between RNA sequences and secondary structures are inves tigated by exhaustive folding of all GC and AU sequences with chain le ngths up to 30. The technique of tries is used for economic data stora ge and fast retrieval of information. The computed structural data are evaluated through exhaustive enumeration and used as an exact referen ce for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA se quence to secondary structure mappings are investigated, among them th e structure of neutral networks (being sets of RNA sequences folding i nto the same structure), percolation of sequence space by neutral netw orks, and the principle of shape space covering. The data of exhaustiv e enumeration are compared to the analytical results of a random graph model that reveals the generic properties of sequence to structure ma ppings based on some base pairing logic. The differences between the n umerical and the analytical results are interpreted in terms of specif ic biophysical properties of RNA molecules.