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Table 2 Evaluation of type II PKS domain classifiers using profiled HMM and sequence pairwise alignment based SVM with 4- fold cross-validation (n > 20) and leave-one-out cross-validation (n < 20)

From: PKMiner: a database for exploring type II polyketide synthases

Domain Subfamily n HMM SVM
    SN (%) SP (%) AC (%) MCC (%) SN (%) SP (%) AC (%) MCC (%)
KS a 43 100 100 100 100 100 100 100 100
CLF a 43 100 100 100 100 100 100 100 100
ACP a 44 100 97.78 98.86 97.75 93.26 97.38 95.23 90.55
KR a 25 100 100 100 100 100 100 100 100
  b 5 100 100 100 100 100 100 100 100
ARO a 29 98.98 100 99.48 98.97 100 93.85 96.72 93.65
  b 29 96.67 90.38 93.3 86.62 100 100 100 100
  c 11 96.67 89.74 93.06 86.41 100 91.67 95.45 91.29
CYC a 19 92.97 84.11 88.03 76.57 100 100 100 100
  b 11 92.97 79.52 85 71.24 100 91.67 95.45 91.29
  c 10 76.7 94.5 83.38 68.95 100 100 100 100
  d 6 93.75 80.45 85.91 73 100 100 100 100
  e 5 77.53 96.29 84.53 71.4 100 100 100 100
  f 6 100 100 100 100 100 75 83.33 70.71
AT a 10 77.76 95.77 84.56 71.28 83.33 100 90 81.65
  1. SN-sensitivity, SP-Specificity, AC-Accuracy, MCC-Matthews correlation coefficient.