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Table 3 Comparison with other methods on the N3D dataset.

From: Improving the prediction of disease-related variants using protein three-dimensional structure

 

Q2

P[D]

S[D]

P[N]

S[D]

C

AUC

PM

SIFT

0.77

0.77

0.74

0.76

0.79

0.53

0.83

96

PolyPhen2

0.80

0.78

0.83

0.82

0.76

0.60

0.86

99

SVM-SEQ

0.80

0.78

0.84

0.82

0.76

0.59

0.86

100

SVM-3D

0.82

0.80

0.85

0.84

0.79

0.63

0.89

100

  1. The accuracy measures are defined in Methods section. D and N are disease-related and neutral variants respectively. PM is the predicted fraction of the dataset. Methods are tested on N3D dataset.
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BMC Bioinformatics

ISSN: 1471-2105

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