Table 1 Prediction for 5' and 3' gene-ends for five programs on test sets. Comparison of prediction for 5' and 3' ends of genes are performed among MED 2.0 (MED), Glimmer 2.02 post-processed by RBSfinder (GL2), Glimmer 3.02 (GL3) GeneMarkS (GMK), ZCURVE 1.0 (ZCV) and EasyGene (EG) on a set of reliable test setsa
From: MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
Test setb | Gene # | 3' end match (%) | Both ends match (%) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | MED | GL2 | GL3 | GMKc | ZCV | EG | MED | GL2 | GL3 | GMKc | ZCV | EG |
Bsub_All | 4100 | 98.7 | 98.2 | 97.6 | 98.9 (96.7) | 98.4 | 94.5 | 83.8 | 75.0 | 82.4 | 86.1 (83.2) | 83.1 | 79.6 |
EcoGene | 854 | 99.1 | 99.3 | 99.4 | 99.9 (-) | 98.8 | 99.4 | 92.0 | 82.5 | 91.9 | 93.8 (-) | 89.2 | 91.1 |
Link | 195 | 99.0 | 100.0 | 100.0 | 100.0 (100.0) | 100.0 | 100.0Â Â | 93.3 | 85.6 | 94.4 | 94.4 (94.4) | 92.3 | 92.1 |
EcoGene_short | 58 | 93.1 | 91.4 | 96.6 | 100.0 (-) | 86.2 | 93.3 | 91.4 | 77.6 | 89.7 | 98.3 (-) | 77.6 | 90.0 |
Bsub123 | 123 | 95.1 | 91.1 | 87.8 | 97.6 (91.9) | 91.9 | 73.0 | 85.4 | 73.2 | 77.2 | 87.8 (82.9) | 78.0 | 66.0 |
Bsub72 | 72 | 94.4 | 91.7 | 87.5 | 98.6 (94.4) | 93.1 | 82.4 | 87.5 | 75.0 | 77.8 | 93.1 (88.9) | 86.1 | 76.5 |
Bsub51 | 51 | 92.2 | 88.2 | 82.3 | 98.0 (94.1) | 90.2 | 84.8 | 90.2 | 70.6 | 78.4 | 94.1(90.2) | 84.3 | 81.8 |
Psaer107 | 107 | 97.2 | 100.0 | 95.3 | 93.5 (-) | 95.3 | 100.0 | 93.5 | 83.2 | 90.6 | 85.0 (-) | 91.6 | 88.0 |
Mtub66 | 66 | 95.5 | 98.5 | 97.0 | 98.5 (-) | 97.0 | 97.5 | 87.9 | 60.6 | 80.3 | 80.3 (-) | 75.8 | 82.5 |
SolfGene | 56 | 100.0 | 100.0 | 100.0 | 100.0 (-) | 100.0 | 100.0 | 89.3 | 50.0 | 87.5 | 85.7 (-) | 73.2 | 89.3 |