95-10-099
Abstract:
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.