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