Table 2.
Sensitivity and specificity for two pseudogene filtering methods
| Experiment | Dataset | Type of mutations | Sensitivity (%) | Specificity (%) | ||
|---|---|---|---|---|---|---|
| ORFfinder | ORFfinder + profile HMM analysis | ORFfinder | ORFfinder + profile HMM analysis | |||
| Artificial DNA barcoding dataset. COI genes and nuMTs from 10 species | Full length COI barcode and nuMT sequences | N/A | 70 | 73 | 90 | 90 |
| Perturbed community dataset | Full length COI barcode and simulated nuMTs | GC—> AT | 31 | 27 | 99 | ~ 100 |
| Perturbed community dataset | Full length COI barcode and simulated nuMTs | Frameshift | 88 | 94 | ~ 100 | ~ 100 |
| Perturbed community dataset | Short COI barcode and simulated nuMTs | GC—> AT | 17**—50* | 6**—15* | 99 | ~ 100 |
| Perturbed community dataset | Short COI barcode and simulated nuMTs | Frameshift | 42**—58* | 61**—87* | 99 | 99*—~ 100** |
| Perturbed community dataset | Full length COI barcode and twice as many nuMTs | GC—> AT | 17 | 0 | 99 | ~ 100 |
| Perturbed community dataset | Full length COI barcode and twice as many nuMTs | Frameshift | 0 | 0 | ~ 100 | ~ 100 |
| Perturbed community dataset | Full length COI barcode and half as many nuMTs | GC—> AT | 39 | 36 | 95 | 96 |
| Perturbed community dataset | Full length COI barcode and half as many nuMTs | Frameshift | 95 | 98 | 96 | 99 |
Sensitivity refers to the true positive rate, our ability to correctly identify known or simulated nuMTs. Specificity refers to the true negative rate, our ability to correctly identify COI genes. * 5’ fragment. ** 3’ fragment