Algorithm Independent Properties of RNA Secondary Structure Predictions
Manfred Tacker, Peter F. Stadler, Erich G. Bornberg-Bauer, Ivo L. Hofacker,
and Peter Schuster
Algorithms predicting RNA secondary structures based on different folding
criteria - minimum free energies (mfe), kinetic folding (kin), maximum
matching (mm) - and different parameter sets are studied systematically.
Two base pairing alphabets were used: the binary GC and the natural
four-letter AUGC alphabet. Computed structures and free energies depend
strongly on both algorithms and parameter sets. Statistical properties,
such as mean numbers of base pairs, mean numbers of stacks, mean loop sizes,
etc., are much less sensitive to the choices of parameter sets and even
algorithms. Some features of RNA secondary structures, like structure
correlation functions, shape space covering and neutral networks, seem
to depend only on the base pairing logic (GC or AUGC alphabet).
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