Combinatorics of RNA Secondary Structures

Ivo L. Hofacker, Peter Schuster, and Peter F. Stadler

Secondary structures of polynucleotides can be view as a certain class of planar vertex-labeled graphs. We construct recursion formulae enumerating various sub-classes of these graphs as well as certain structural elements (sub-graphs). First order asymptotics are derived and their dependence on the logic of base pairing is computed and discussed.

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