Algorithm Independence Properties and RNA Secondary Structure Predicions

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).