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Table 1 Comparison between feature-based and general localization tools according to the validation metrics.

From: Validating subcellular localization prediction tools with mycobacterial proteins

  Feature-based tools General localization tools
Parameters SignalP 2.0, TatP 1.0, LipoP 1.0 SignalP 2.0 Phobius PA-SUB 2.5 Gpos-PLoc PSORTb v.2.0.4
TPs 91 87 55 204 147 145
TNs 65 65 64 68 53 56
FPs 3 3 4 0 14 1.0
FNs 113 117 149 0 57 14
Specificity 0.97 0.97 0.93 1.0 0.91 0.99
Sensitivity 0.45 0.43 0.27 1.0 0.72 0.91
MCC 0.37 0.35 0.22 1.0 0.45 0.84
  Summatory
Secreted (TPs+FNs) 204 204 204 204 204 159
Non secreted (TNs+FPs) 68 68 68 68 67 57
  1. TPs, True Positives. TNs, True Negatives. FPs, False Positives. FNs, False Negatives. Secreted proteins (n = 204), non-secreted proteins (n = 68), N = 272