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Table 1 Comparing the error detection performance of HMM-FRAME, Genewise, and FragGeneScan

From: HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors

  HMM-FRAME:
G20
HMM-FRAME:
self-trained
GeneWise FragGeneScan
seq-sen 95.25% 90.6% 53.8% 83.04%
base-sen 85.08% 82.4%   53.39%
seq-FP 0.154% 0 0.001% 0.7%
base-FP 2.1% 0.003%   59.57%
  1. Sensitivity and FP rate of each program when detecting annotated insertion and deletion errors in nifH genes. seq-sen: sequence-level sensitivity. base-sen: base-level sensitivity. seq-FP: sequence-level FP rate. base-FP: base-level FP rate. The score cutoff of Genewise is set to zero to maximize the sensitivity. As Genewise has low sequence-level sensitivity, we did not evaluate its performance at the base-level.