Table 3.
Values of nucleotide level sensitivity and specificity (Sn/Sp) along with (Sn + Sp)/2 for gene predictions produced by GeneMark.hmm and SNAP for the group of ‘well-known’ genomes
| GeneMark.hmm unsupervised (ES-3.0) | SNAP bootstrap | GeneMark.hmm supervised (E-3.0) | SNAP supervised | GenScan supervised | Genefinder supervised | Augustus supervsed | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A.thaliana | 98.3 | 96.5 | 96.6 | 94.9 | 98.4 | 96.3 | 97.1 | 96.2 | 79.9 | 86.4 | – | – | – | – |
| 94.7 | 93.2 | 94.2 | 95.2 | 92.9 | – | – | ||||||||
| C.elegans | 99.1 | 97.1 | 96.7 | 93.9 | 97.7 | 97.0 | 97.6 | 95.9 | – | – | 98.1 | 96.7 | – | – |
| 95.1 | 91.1 | 96.2 | 94.2 | – | 95.3 | – | ||||||||
| D.melanogaster | 93.8 | 90.0 | 92.5 | 89.6 | 93.2 | 90.5 | 94.3 | 90.4 | – | – | – | – | 92.4 | 90.5 |
| 86.1 | 86.6 | 87.7 | 86.5 | – | – | 88.6 | ||||||||
The unsupervised mode of GeneMark.hmm (ES-3.0) is compared with the bootstrapped mode of SNAP (first two columns). The performance of the supervised modes of the two programs, GeneMark.hmm E-3 and SNAP, are also com pared (last five columns) with performance of GenScan (trained on A.thaliana), Genefinder (trained on C.elegans) and Augustus (trained on D.melanogaster). All figures in this table, except ones for GeneMark.hmm, are cited from (6). The accuracy of GeneMark.hmm was assessed on the same test sets downloaded from the SNAP website.