Table 1 Benchmarking whole-genome TE annotations on plant and animal genomes including chicken, fly, maize, mouse, rice, zebrafish, and zebra finch
Category | TE | Benchmark | EDTAa | EDTA_repbaseb | EDTA_repeatmodeler2c | RepeatModeler2d |
|---|---|---|---|---|---|---|
Animals | LTR | Sensitivity | 63.3% | 57.6% | 72.2% | 81.4% |
Animals | non-LTR | Sensitivity | 1.0% | 43.7% | 66.9% | 76.1% |
Animals | TIR | Sensitivity | 38.8% | 35.1% | 40.9% | 38.9% |
Plants | LTR | Sensitivity | 94.7% | 94.6% | 94.7% | 73.5% |
Plants | non-LTR | Sensitivity | 0.0% | 82.2% | 49.6% | 57.5% |
Plants | TIR | Sensitivity | 67.1% | 66.8% | 67.1% | 28.1% |
Animals | LTR | Specificity | 95.0% | 97.8% | 96.9% | 96.8% |
Animals | non-LTR | Specificity | 100.0% | 98.2% | 98.7% | 97.9% |
Animals | TIR | Specificity | 88.4% | 91.7% | 89.8% | 97.4% |
Plants | LTR | Specificity | 90.4% | 90.7% | 90.5% | 97.9% |
Plants | non-LTR | Specificity | 100.0% | 99.6% | 99.9% | 99.9% |
Plants | TIR | Specificity | 94.7% | 95.1% | 94.8% | 99.6% |