Table 2.
Gene-finding performance for various algorithms.
| Gene | Transcript | Exon | ||||||||||||
| ALL | initial | internal | terminal | single | ||||||||||
| sn% | sp% | sn% | sp% | sn% | sp% | sn% | sp% | sn% | sp% | sn% | sp% | sn% | sp% | |
| Augustus | 47.0 | 50.9 | 37.6 | 50.9 | 70.8 | 78.8 | 53.5 | 66.4 | 77.6 | 81.8 | 70.9 | 83.2 | 61.9 | 72. |
| CONTRAST | 48.8 | 51.9 | 39.2 | 51.9 | 69.7 | 80.8 | 57.4 | 70.6 | 74.2 | 84.6 | 69.7 | 80.8 | 68.9 | 78.0 |
| Geneid | 35.9 | 41.4 | 29.3 | 41.4 | 65.7 | 71.4 | 47.0 | 60.9 | 75.6 | 73.9 | 59.2 | 72.8 | 54.6 | 73.7 |
| Genie | 40.7 | 50.0 | 31.9 | 50.0 | 58.2 | 77.9 | 44.1 | 63.7 | 63.1 | 82.7 | 58.8 | 80.2 | 58.7 | 68.8 |
| Genscan | 31.4 | 35.7 | 24.9 | 35.7 | 61.3 | 61.6 | 42.4 | 54.6 | 70.8 | 61.6 | 54.1 | 65.9 | 58.7 | 76.9 |
| Evigan-5g | 54.6 | 58.9 | 43.8 | 58.9 | 73.7 | 84.4 | 61.0 | 74.6 | 78.7 | 87.5 | 72.9 | 84.6 | 70.7 | 85.6 |
| ReRanker-5g | 57.6 | 62.1 | 46.1 | 62.1 | 74.2 | 85.4 | 61.8 | 75.9 | 79.0 | 88.5 | 73.9 | 85.9 | 71.6 | 86.3 |
| GeneWise | 29.4 | 31.0 | 25.0 | 31.0 | 58.3 | 73.9 | 41.8 | 56.7 | 69.5 | 90.9 | 48.5 | 59.4 | 32.3 | 30.6 |
| Augustus+ | 53.3 | 57.0 | 43.5 | 57.0 | 73.0 | 81.1 | 58.3 | 72.2 | 79.2 | 84.0 | 71.6 | 83.3 | 65.2 | 73.0 |
| Evigan-6g | 56.3 | 60.7 | 45.1 | 60.7 | 74.7 | 85.2 | 61.4 | 75.4 | 80.2 | 88.3 | 73.5 | 85.7 | 70.5 | 84.7 |
Performance on the entire D. melanogaster test set of 7777 loci (see Table 1). Augustus, CONTRAST, Geneid, Genie and Genscan are ab initio predictors used as evidence sources for Evigan-5g. ReRanker-5g selects among K-best gene models produced by Evigan-5g with cross-species information. GeneWise, Augustus+ and Evigan-6g are other comparative gene predictors or approaches. Bold indicates where ReRanker-5g outperforms Evigan-5g; italics indicates where other comparative approaches outperform ReRanker-5g (see text).