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Table 2 Evaluation of type II PKS domain classifiers using profiled HMM and sequence pairwise alignment based SVM with 4- fold cross-validation (n > 20) and leave-one-out cross-validation (n < 20)

From: PKMiner: a database for exploring type II polyketide synthases

Domain

Subfamily

n

HMM

SVM

   

SN (%)

SP (%)

AC (%)

MCC (%)

SN (%)

SP (%)

AC (%)

MCC (%)

KS

a

43

100

100

100

100

100

100

100

100

CLF

a

43

100

100

100

100

100

100

100

100

ACP

a

44

100

97.78

98.86

97.75

93.26

97.38

95.23

90.55

KR

a

25

100

100

100

100

100

100

100

100

 

b

5

100

100

100

100

100

100

100

100

ARO

a

29

98.98

100

99.48

98.97

100

93.85

96.72

93.65

 

b

29

96.67

90.38

93.3

86.62

100

100

100

100

 

c

11

96.67

89.74

93.06

86.41

100

91.67

95.45

91.29

CYC

a

19

92.97

84.11

88.03

76.57

100

100

100

100

 

b

11

92.97

79.52

85

71.24

100

91.67

95.45

91.29

 

c

10

76.7

94.5

83.38

68.95

100

100

100

100

 

d

6

93.75

80.45

85.91

73

100

100

100

100

 

e

5

77.53

96.29

84.53

71.4

100

100

100

100

 

f

6

100

100

100

100

100

75

83.33

70.71

AT

a

10

77.76

95.77

84.56

71.28

83.33

100

90

81.65

  1. SN-sensitivity, SP-Specificity, AC-Accuracy, MCC-Matthews correlation coefficient.