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Table 1 Comparison of 12 different methods for mutation analysis

From: Status quo of annotation of human disease variants

Method Pathogenic mutants SNPs Based on
Grantham [13] 67,4 65,2 AA differences
PhD-SNP [16] 85,6 73,9 Conservation
Panther [15] 86,5 35,1 Conservation
SIFT [14] 87,8 64,4 Conservation
SNPs&GO [20] 72,5 77,8 Conservation, GO terms
SNAP [19] 83,4 56,5 Conservation, sequence predicted structure information
MutPred [21] 92,8 85,7 Conservation, sequence predicted structure information
nsSNPanalyzer [24] 74,5 67,6 Conservation, 3D structural features from homologs, AA properties
SNPs3D [22] 86,3 62,8 Conservation, structure information (pre-calculated from database)
PolyPhen-2 [32] 95,0 58,6 Conservation, 3D structural features from homologs, SwissProt annotations
HOPE [35] 96,1 76,1 Conservation, structural features from structure and homology models, SwissProt features, predictions, AA properties
  1. Results of the mutation analysis on 181 pathogenic and 46 neutral variants by 11 different methods. Pathogenic mutants and SNPs are shown in percentage of correctly predicted cases. The numbers indicate percentages correctly (damaging for the pathogenic variants and benign for the SNPs) predicted mutations.