Table 2.
Predictive accuracies of MEGANTE and individual gene prediction programs used in the system
| Test gene sets | Evaluation categories | MEGANTE | AUGUSTUS | GeneZilla | GlimmerHMM | SNAP | |
|---|---|---|---|---|---|---|---|
| A. thaliana | Exon level | Sn (%) | 95.2 | 84.4 | 71.8 | 80.9 | 75.5 |
| Sp (%) | 87.9 | 75.6 | 66.5 | 72.7 | 59.2 | ||
| Gene level | Sn (%) | 84.2 | 58.4 | 43.6 | 49.1 | 38.7 | |
| Sp (%) | 58.8 | 43.4 | 28.0 | 35.2 | 22.4 | ||
| G. max | Exon level | Sn (%) | 78.8 | 75.3 | 57.5 | 56.3 | 61.8 |
| Sp (%) | 86.7 | 71.1 | 54.2 | 59.1 | 54.3 | ||
| Gene level | Sn (%) | 51.4 | 35.9 | 22.1 | 28.2 | 18.2 | |
| Sp (%) | 48.8 | 32.5 | 13.6 | 16.0 | 12.1 | ||
| M. acuminata | Exon level | Sn (%) | 46.1 | 48.3 | 19.9 | 34.7 | 30.5 |
| Sp (%) | 62.3 | 54.4 | 28.7 | 31.5 | 36.4 | ||
| Gene level | Sn (%) | 12.8 | 12.2 | 5.9 | 7.6 | 5.8 | |
| Sp (%) | 12.7 | 11.2 | 4.1 | 3.4 | 4.0 | ||
| O. sativa | Exon level | Sn (%) | 91.9 | 52.9 | 57.0 | 74.0 | 45.4 |
| Sp (%) | 86.7 | 67.4 | 46.4 | 59.0 | 50.6 | ||
| Gene level | Sn (%) | 78.0 | 29.5 | 21.9 | 37.8 | 19.7 | |
| Sp (%) | 57.1 | 29.3 | 12.2 | 21.6 | 15.6 | ||
| P. trichocarpa | Exon level | Sn (%) | 76.7 | 73.7 | 60.8 | 55.0 | 63.4 |
| Sp (%) | 81.1 | 71.0 | 57.8 | 59.3 | 57.4 | ||
| Gene level | Sn (%) | 32.3 | 26.8 | 19.6 | 21.4 | 14.4 | |
| Sp (%) | 32.0 | 25.8 | 13.4 | 13.2 | 10.7 | ||
| S. lycopersicum | Exon level | Sn (%) | 85.7 | 69.4 | 49.0 | 49.3 | 57.0 |
| Sp (%) | 91.1 | 74.4 | 49.1 | 52.4 | 49.3 | ||
| Gene level | Sn (%) | 62.6 | 29.5 | 22.0 | 26.8 | 19.3 | |
| Sp (%) | 60.0 | 34.0 | 13.0 | 14.5 | 12.3 | ||
| M.×domestica | Exon level | Sn (%) | 59.0 | 59.1 | 47.1 | 49.8 | 42.3 |
| Sp (%) | 68.5 | 62.5 | 47.3 | 50.1 | 46.1 | ||
| Gene level | Sn (%) | 22.1 | 22.5 | 13.2 | 19.1 | 11.2 | |
| Sp (%) | 19.0 | 18.4 | 7.7 | 9.7 | 7.8 | ||
| V. vinifera | Exon level | Sn (%) | 61.0 | 51.4 | 46.8 | 35.8 | 41.7 |
| Sp (%) | 83.7 | 51.2 | 38.5 | 31.0 | 36.0 | ||
| Gene level | Sn (%) | 22.7 | 10.5 | 7.1 | 6.6 | 5.0 | |
| Sp (%) | 27.3 | 7.9 | 3.5 | 2.6 | 2.6 | ||
Gene prediction parameters we used for each target species are described in the Materials and Methods.