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Table 2 Comparison of algorithms tested on Swiss-Prot dataset*

From: EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome

 

AUC

Accuracy

Precision

Sensitivity

Specificity

EFIN (Swiss-Prot)**

90.7%(1.0%)

83.7%(0.98%)

86.7%(3.3%)

86.4%(0.9%)

79.5%(3.0%)

GERP++

76.10%

52.80%

45.27%

96.78%

24.36%

PhyloP

76.30%

54.47%

46.18%

96.47%

27.33%

MutationTaster

85.40%

79.47%

69.07%

86.42%

74.98%

SIFT

83.60%

76.58%

67.29%

78.52%

75.32%

  1. *This test is based on a subset of Swiss-Prot, of which mutations can be processed by all these 5 tools, including totally 18660 damaging variants and 28863 neutral variants.
  2. **Swiss-Prot trained EFIN is validated by 10 fold cross-validation, and all these statistical measures are average values. Standard deviation is described within brackets after each measure.