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. 2017 Dec 21;34(10):1690–1696. doi: 10.1093/bioinformatics/btx818

Table 3.

Comparative benchmark of different methods in signal peptide detection and cleavage site prediction on the SPDS17 independent dataset

Method Eukaryotes
 Gram-positive
 Gram-negative
MCC FPRT F1cs MCC FPRT F1cs MCC FPRT F1cs
SPOCTOPUS 0.54 16.7 0.20 0.28 20.2 0.37 0.63 14.3 0.12
PRED-TAT 0.55 9.3 0.33 0.26 2.2 0.72 0.82 9.9 0.14
Philius 0.62 6.5 0.46 0.31 3.4 0.72 0.87 7.4 0.22
PolyPhobius 0.73 7.4 0.42 0.44 11.2 0.53 0.80 7.9 0.06
TOPCONS2.0 0.74 5.3 0.27 0.49 4.5 0.60 0.91 2.6 0.08
SignalP4.1 0.82 4.0 0.69 0.50 0.0 0.79 0.93 4.2 0.33
DeepSig 0.86 2.5 0.72 0.54 0.0 0.82 0.95 2.6 0.36

Note: MCC, Matthews Correlation Coefficient; FPRT, False Positive Rate on transmembrane proteins; F1cs, The harmonic mean between precision and recall on cleavage-site detection.