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Table 3 Comparison between EpiJen, NetCTL, WAPP and SMM on HIV epitopes, binding to HLA-A*01, HLA-A*02 and HLA-A*03.

From: EpiJen: a server for multistep T cell epitope prediction

  p17 p24 protease RT integrase rev tat vif vpr vpu gp160 nef total
A*01 1 0 0 0 0 1 0 0 0 0 1 1 4
A*02 2 9 2 11 3 3 0 3 4 1 20 8 66
A*03 2 2 1 9 2 2 1 2 0 0 4 4 29
total 5 11 3 20 5 6 1 5 4 1 25 13 99
EpiJen
TP 5 7 2 14 2 5 1 3 2 0 14 6 61
FN 0 4 1 6 3 1 0 2 2 1 11 7 38
FP 16 17 8 42 26 13 4 17 3 4 115 24 289
Sensitivity % 100 64 67 70 40 83 100 60 50 0 56 46 62
PPV % 24 29 20 25 7 28 20 15 40 0 11 20 17
NetCTL
TP 4 6 1 10 3 3 1 4 1 0 12 4 49
FN 1 5 2 10 2 3 0 1 3 1 13 9 50
FP 8 10 6 39 22 5 7 11 4 2 60 14 188
Sensitivity % 80 55 33 50 60 50 100 80 25 0 48 31 50
PPV % 33 38 14 20 12 38 13 27 20 0 17 22 21
WAPP
TP 2 2 2 7 1 4 0 3 3 0 8 1 33
FN 3 9 1 13 4 2 1 2 1 1 17 12 66
FP 8 6 4 40 13 6 2 13 0 6 61 7 166
Sensitivity % 40 18 67 35 20 67 0 60 75 0 32 8 33
PPV % 20 25 33 15 7 40 0 19 100 0 12 13 17
SMM
TP 3 6 2 15 5 4 0 3 2 0 14 3 57
FN 2 5 1 5 0 2 1 2 2 1 11 10 42
FP 15 18 8 41 23 14 5 17 3 4 115 27 290
Sensitivity % 60 55 67 75 100 67 0 60 50 0 56 23 58
PPV % 17 25 20 27 18 22 0 15 40 0 11 10 16