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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