Table 4.
Values of sensitivity and specificity (Sn/Sp) along with (Sn + Sp)/2 for gene predictions produced by GeneMark.hmm and SNAP for the test sets described in the Dataset section
| A.thaliana | A.gambiae | C.intestinalis | C.elegans | D.melanogaster | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GeneMark.hmm unsupervised | SNAP supervised | GeneMark.hmm unsupervised | SNAP supervised | GeneMark.hmm unsupervised | SNAP supervised | GeneMark.hmm unsupervised | SNAP supervised | GeneMark.hmm unsupervised | SNAP supervised | |||||||||||
| Nucleotide | 97.7 | 96.3 | 93.6 | 94.5 | 96.0 | 90.5 | 87.6 | 84.5 | 98.3 | 94.2 | 90.1 | 82.2 | 99.1 | 96.4 | 97.2 | 95.7 | 97.9 | 95.4 | 94.8 | 93.9 |
| 94.8 | 95.3 | 85.0 | 81.4 | 90.0 | 74.3 | 93.6 | 94.1 | 92.9 | 92.9 | |||||||||||
| Internal | 91.2 | 89.5 | 79.7 | 83.8 | 89.3 | 88.9 | 81.7 | 84.7 | 94.8 | 93.5 | 80.9 | 71.3 | 94.0 | 92.7 | 87.1 | 87.1 | 91.3 | 90.5 | 85.8 | 85.5 |
| exons | 87.8 | 87.8 | 88.4 | 87.6 | 92.1 | 61.7 | 91.3 | 87.1 | 89.7 | 85.2 | ||||||||||
| Initiation | 80.1 | 78.3 | 75.6 | 75.0 | 77.8 | 72.9 | 65.2 | 66.2 | 79.6 | 71.3 | 61.0 | 52.2 | 85.8 | 77.4 | 73.2 | 67.4 | 83.9 | 78.7 | 78.1 | 77.7 |
| sites | 76.5 | 74.3 | 67.9 | 67.2 | 63.0 | 43.4 | 68.9 | 61.5 | 73.5 | 77.3 | ||||||||||
| Termination | 87.5 | 85.3 | 84.0 | 83.5 | 86.1 | 78.9 | 78.8 | 76.0 | 85.4 | 75.9 | 63.3 | 54.6 | 95.1 | 85.2 | 89.4 | 80.9 | 89.2 | 83.2 | 78.1 | 77.5 |
| sites | 83.1 | 82.9 | 71.7 | 73.2 | 66.3 | 45.9 | 75.3 | 72.4 | 77.2 | 76.8 | ||||||||||
| Donor sites | 94.0 | 92.2 | 83.7 | 86.9 | 89.7 | 86.9 | 80.8 | 83.1 | 95.3 | 92.5 | 82.7 | 72.6 | 96.2 | 93.5 | 90.1 | 89.0 | 92.8 | 90.0 | 86.9 | 86.6 |
| 90.3 | 90.0 | 84.1 | 85.3 | 89.7 | 62.4 | 90.8 | 87.8 | 87.2 | 86.2 | |||||||||||
| Acceptor | 94.0 | 92.1 | 84.6 | 87.8 | 92.3 | 88.5 | 83.3 | 83.7 | 96.3 | 93.3 | 83.6 | 73.5 | 97.3 | 94.5 | 93.5 | 92.1 | 93.0 | 90.0 | 87.7 | 87.3 |
| sites | 90.2 | 91.0 | 84.7 | 84.1 | 90.3 | 63.3 | 91.6 | 90.6 | 87.0 | 86.8 | ||||||||||
The unsupervised mode of Gene-Mark.hmm (ES-3.0) is compared with the supervised mode of SNAP which typically performs better than the SNAP bootstrapped mode (6). The supervised models from SNAP were downloaded from the SNAP website (see text).