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Table 1 Prediction quality of the profile-based methods

From: The value of position-specific scoring matrices for assessment of protein allegenicity

Method E-value threshold FN FP ACC (%) SP (%) SE (%) PPV (%) NPV (%) MCC
General Profile 10 11 1792 21.67 10.38 96.42 13.99 94.71 0.08
  1 22 737 67.03 63.17 92.58 27.74 98.25 0.38
  10-1 31 298 85.72 85.11 89.80 48.45 98.22 0.59
  10-2 36 184 90.42 90.80 87.95 60.22 98.03 0.68
  10-3 41 137 92.27 93.14 86.56 66.70 97.87 0.72
  10-4 43 108 93.44 94.61 85.70 71.76 97.77 0.75
  10-6 48 83 94.32 95.87 84.04 76.53 97.55 0.77
  10-9 53 62 95.02 96.92 82.45 81.34 97.34 0.79
Group-Specific 10 14 1801 21.14 9.92 95.43 13.79 93.48 0.06
Profiles 1 22 748 66.53 62.58 92.72 27.33 98.27 0.38
  10-1 29 317 84.99 84.17 90.40 46.88 98.31 0.58
  10-2 34 202 89.76 89.89 88.87 57.87 98.16 0.66
  10-3 37 151 91.83 92.44 87.81 64.73 98.04 0.71
  10-4 40 124 92.86 93.79 86.69 68.87 97.90 0.73
  10-6 44 94 94.02 95.31 85.50 74.51 97.75 0.76
  10-9 48 70 94.88 96.52 84.04 79.49 97.56 0.79