From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures
Peter Schuster, Walter Fontana, Peter F. Stadler, and Ivo L. Hofacker
RNA folding is viewed as a map assigning secondary structures to sequences. At
fixed chain length the number of sequences exceeds by far the number of
structures. Frequencies of structures are highly non-uniform: we find
relatively few common and many rare ones. Using an algorithm for inverse
folding we show that sequences sharing the same structures are distributed
randomly over sequences space. All common structures can be accessed from an
arbitrary sequence by a number of mutations much smaller than the chain
length. Evolutionary optimization has to search only a small fraction of all
sequences in order to find a suitable target structure and thus could hardly
miss it. The sequence space is percoated by extensive neutral networks
connecting nearest neighbours folding into identical structures.
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