. 2006 Jul 14;34(Web Server issue):W182–W185. doi: 10.1093/nar/gkl189

Table 3.

Performance measure (Q₃ and Q_p scores) for the three-class prediction of LC, HC, FC using different kernels and input representation

Kernel	Q₃			Q_p
	SpR	MmR	PrfR	SpR	MmR	PrfR
Linear	0.75	0.64	0.63	0.45	0.43	0.43
Polynomial (2)	0.78	0.74	0.74	0.53	0.46	0.45
Polynomial (3)	0.76	0.72	0.72	0.5	0.47	0.47
RBF	0.75	0.73	0.72	0.43	0.43	0.43

The Q₃ score is the ratio between correct prediction and total number of examples. The Q_p score is the fraction of proteins for which all cysteines are correctly predicted. Q₃ and Q_p scores are obtained averaging the results of a 5-fold cross validation. Optimal values of the C parameter and the γ parameter for the radial basis function (RBF) kernel are estimated by a grid search. Legend: SpR—Spectrum representation; MmR—Mismatch representation; PrfR—Profile representation.