Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration

Walter Gruner, Robert Giegerich, Dirk Strothmann, Christian Reidys, Jacqueline Weber, Ivo L. Hofacker, Peter F. Stadler, and Peter Schuster

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 technique of tried is used for economic data storage and fast retrieval of information. 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 of statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them the structure of neural networks (being sets of sequences folding into the same structure), percolation of sequence space by neural networks, and the principle of shape space covering. The data of exhaustive enumeration are compared to the analytical results of a random graph model that reveals the generic properties of sequence to structure mappings based on some base pairing logic. The differences between the numerical and the analytical results are interpreted in terms of specific biophysical properties of RNA molecules.

Return to 1995 working papers list.