Table 2.

Topology-to-topology SVM training and test performance using as input the output of the sequence-to-topology SVM. "With" and "Without Structure II" indicates if the predicted secondary structure of the sequence is also included in input or not. LRG and PHAT columns correspond to the substitution matrices used by the sequence-to-topology SVM.

	Without Structure II		With Structure II
Substitution Matrix	LRGa	PHATb	LRGc	PHATd
Accuracy	91.7	93.6	92.3	94.3
Sensitivity	42.9	64.3	41.1	44.1
Specificity	95.5	95.9	96.4	98.3
Pnon-IPM	95.4	97.1	95.3	95.6
PIPM	44.1	55.7	47.5	67.1
CPM	0.39	0.64	0.40	0.52

^a C = 10.0, 1/2σ² = 0.1, predictors = segment of 21 residues

^b C = 10.0, 1/2σ² = 0.1, predictors = segment of 21 residues

^c C = 15.0, 1/2σ² = 0.1, predictors = segment of 21 residues + corresponding predicted secondary structure

^d C = 5.0, 1/2σ² = 0.05, predictors = segment of 21 residues + corresponding predicted secondary structure.