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Table 2 The performance on the Eukaryotes datasets

From: SigUNet: signal peptide recognition based on semantic segmentation

Method

MCC (%)

FPRTM (%)

Precision (%)

Recall (%)

F1 measure (%)

The SignalP dataset

 Phobius

81.1

15.3

77.6

95.2

85.5

 PrediSi

56.1

52.6

52.0

91.3

66.3

 SignalP3.0-HMM

75.9

23.5

69.5

97.4

81.1

 SignalP3.0-NN

56.2

64.1

48.4

98.8

65.0

 PolyPhobius

80.6

12.5

79.5

91.9

85.2

 Philius

80.4

13.4

77.8

93.7

85.0

 SPOCTOPUS

80.1

14.0

79.0

91.7

84.9

 SignalP 4.0

87.4

6.1

–

–

–

 TOPCONS2

84.6

9.6

83.6

93.6

88.3

 DeepSig

87.2

4.2

92.5

87.8

90.1

 SigUNet

90.2

4.0

93.0

92.1

92.5

The SPDS17 dataset

 Phobius

65.8

9.6

47.8

95.7

63.8

 PrediSi

38.5

43.3

20.7

89.1

33.6

 SignalP3.0-HMM

51.6

22.3

31.2

95.7

47.1

 SignalP3.0-NN

36.0

59.1

17.5

95.7

29.5

 PolyPhobius

72.0

8.0

56.4

95.7

71.0

 Philius

62.3

6.5

44.3

93.5

60.1

 SPOCTOPUS

54.0

16.4

37.9

84.8

52.3

 SignalP 4.0

81.9

4.0

75.0

91.3

82.3

 TOPCONS2

73.9

5.6

60.6

93.5

73.5

 DeepSig

86.1

2.5

82.4

91.3

86.6

 SigUNet

89.6

1.2

91.1

89.1

90.1

  1. The performances of Phoibus, PrediSi and SignalP 3.0 are obtained from their online services (Phobius: http://phobius.sbc.su.se/; PrediSi: http://www.predisi.de/predisi/; SignalP 3.0: http://www.cbs.dtu.dk/services/SignalP-3.0/) [11, 23, 24]. The performances of PolyPhobius, Philius, SPOCTOPUS and TOPCONS2 are obtained from the TOPCONS2 software (https://github.com/ElofssonLab/TOPCONS2) [25,26,27,28]. The performance of SignalP 4.0 on the SignalP dataset is obtained from the original paper [12] and the performance on the SPDS17 dataset is obtained from its online service (http://www.cbs.dtu.dk/services/SignalP-4.0/). The performance of DeepSig on the SignalP dataset is obtained by reproducing the algorithm and the performance on the SPDS17 dataset is obtained using the source code (https://github.com/BolognaBiocomp/deepsig). For each dataset, the best performance is highlighted in bold.