Skip to main content

Table 3 Comparison of UProC, HMM-GRASPx and MetaCLADE on the Guerrero Negro Hypersaline microbial Mat project (100-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

323 659

31 539

357 182

47.5

91.1

62.5

 MetaCLADE

291 896

57 955

388 945

42.9

83.4

56.6

 HMM-GRASPx

325 689

41 155

355 152

47.8

88.8

62.2

 MetaCLADE+UProC

370 274

72 132

310 567

54.4

83.7

65.9

 UProC+MetaCLADE

378 449

70 063

302 392

55.6

84.4

67.0

 UProC clan

328 910

26 288

351 931

48.3

92.6

63.5

 MetaCLADE clan

309 629

40 222

371 212

45.5

88.5

60.1

 HMM-GRASPx clan

334 480

32 364

346 361

49.1

91.2

63.9

 MetaCLADE+UProC clan

389 454

52 952

291 387

57.2

88.0

69.3

 UProC+MetaCLADE clan

390 388

58 124

290 453

57.3

87.0

69.1

CLADE gold standard

 UProC

308 483

48 077

476 068

39.3

86.5

54.1

 MetaCLADE

286 458

48 696

498 093

36.5

85.5

51.2

 HMM-GRASPx

296 742

69 211

487 809

37.8

81.1

51.6

 MetaCLADE+UProC

361 794

64 085

422 757

46.1

85.0

59.8

 UProC+MetaCLADE

366 221

66 114

418 330

46.7

84.7

60.2

 UProC clan

336 302

20 258

448 249

42.9

94.3

58.9

 MetaCLADE clan

323 009

12 145

461 542

41.2

96.4

57.7

 HMM-GRASPx clan

328 729

37 224

455 822

41.9

89.8

57.1

 MetaCLADE+UProC clan

405 734

20 145

378 817

51.7

95.3

67.0

 UProC+MetaCLADE clan

406 370

25 965

378 181

51.8

94.0

66.8

  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