Table 3.

Comparison of EFIN with PolyPhen-2 on a subset of Swiss-Prot variants

Tools (Training set)	AUC	Accuracy	Precision	Sensitivity	Specificity
Testing set: Swiss-Prot dataset with HumDiv mutations excluded (36998 neutral variants, 17643 damaging variants)*
EFIN (HumDiv)	86.96%	80.71%	85.96%	84.96%	72.16%
polyphen2 (HumDiv)	85.26%	78.35%	63.27%	78.59%	78.24%
Testing set: Swiss-Prot dataset with HumVar mutations excluded (15819 neutral variants, 2284 damaging variants)*
EFIN (Swiss-Prot ∩ HumVar)**	84.91%	71.37%	96.72%	69.60%	83.64%
polyphen2 (HumVar)	80.60%	78.09%	32.28%	67.12%	79.67%

*This test is based on a subset of Swiss-Prot dataset of which mutations can be processed by both EFIN and PolyPhen-2.

**EFIN is trained by intersection of HumVar and Swiss-Prot datasets.