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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