Dependence of RNAalifold on the weights β and δ.A: For all three RNAalifold variants, the accuracy of the structure prediction, measured here as MCC for the CMfinder-SARSE dataset (Table 1), depends on the weight β of the covariance term (δ = 0.6). B: The AUC value for the SCI computation also depends strongly on the values of β and δ. The green square indicates the optimal parameters (β = 1.55, δ = 0.6), the red dot is the default (1, 1). As the default is close to the maximum, there is little room for improvement.
Bernhart et al. BMC Bioinformatics 2008 9:474 doi:10.1186/1471-2105-9-474