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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