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Table 4 Comparison of UProC, HMM-GRASPx and MetaCLADE on the Guerrero Negro Hypersaline microbial Mat project (200-bp reads)

From: A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

Tool

TP

FP

FN

Recall

Precision

F-score

Pfam gold standard

 UProC

252 245

28 101

161 239

61.0

90.0

72.7

 MetaCLADE

307 711

50 380

105 773

74.4

85.9

79.8

 HMM-GRASPx

288 152

38 152

125 332

69.7

88.3

77.9

 MetaCLADE+UProC

319 829

55 189

93 655

77.3

85.3

81.1

 UProC+MetaCLADE

326 133

56 556

87 351

78.9

85.2

81.9

 UProC clan

256 847

23 499

156 637

62.1

91.6

74.0

 MetaCLADE clan

326 217

31 874

87 267

78.9

91.1

84.6

 HMM-GRASPx clan

293 267

33 037

120 217

70.9

89.9

79.3

 MetaCLADE+UProC clan

338 609

36 409

74 875

81.9

90.3

85.9

 UProC+MetaCLADE clan

339 285

43 404

74 199

82.1

88.7

85.2

CLADE gold standard

 UProC

240 762

43 085

244 393

49.6

84.8

62.6

 MetaCLADE

302 583

63 491

182 572

62.4

82.7

71.1

 HMM-GRASPx

262 511

64 833

222 644

54.1

80.2

64.6

 MetaCLADE+UProC

316 656

68 490

168 499

65.3

82.2

72.8

 UProC+MetaCLADE

322 760

70 325

162 395

66.5

82.1

73.5

 UProC clan

264 787

19 060

220 368

54.6

93.3

68.9

 MetaCLADE clan

347 936

18 138

137 219

71.7

95.0

81.7

 HMM-GRASPx clan

290 155

37 189

195 000

59.8

88.6

71.4

 MetaCLADE+UProC clan

363 667

21 479

121 488

75.0

94.4

83.6

 UProC+MetaCLADE clan

364 641

28 444

120 514

75.2

92.8

83.0

  1. The first table considers Pfam27 annotations as gold standard, while the second one uses CLADE27. Each table is made of two sub-tables where we evaluate annotation on exact domains (top) and on clans (bottom). Annotations with domains of the same clan are counted as true positives
  2. Largest values are reported in italics