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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.

From: Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier

  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
  1. a C = 10.0, 1/2 σ2 = 0.1, predictors = segment of 21 residues
  2. b C = 10.0, 1/2 σ2 = 0.1, predictors = segment of 21 residues
  3. c C = 15.0, 1/2 σ2 = 0.1, predictors = segment of 21 residues + corresponding predicted secondary structure
  4. d C = 5.0, 1/2 σ2 = 0.05, predictors = segment of 21 residues + corresponding predicted secondary structure.