MCC on the CMfinder-SARSE dataset as a function of the β and δ parameters. It can be seen that except for β = 1.0, using RIBOSUM Matrices improves the performance of the new RNAalifold, which is in turn always better than the 2002 (old) variant. Furthermore, for the RIBOSUM variant, the size of the plateau, i.e. the subset of parameters with a MCC ≥ 0.93 is quite big, containing 36 of 100 combinations of parameters (80 are ≥ 0.9, 21 are ≥ 0.935 and 6 are 0.937). Top: 3d-plot of the MCC against the parameters β and δ. Bottom: Vertical section along the diagonals β = δ and δ + β = 1.1.
Bernhart et al. BMC Bioinformatics 2008 9:474 doi:10.1186/1471-2105-9-474