Table 3 Gene Prediction Performance
From: Prodigal: prokaryotic gene recognition and translation initiation site identification
| Organism | %GC | Verified | Prodigal 1.20 | Prodigal 1.20+TriTisa | Prodigal 1.20+TiCo | GeneMarkHMM 2.6 | EasyGene 1.2 | Glimmer 3.02 | MED 2.0 |
|---|---|---|---|---|---|---|---|---|---|
| Escherichia coli K12 | 50.8 | 884 |
884/853 (100%/96.5%) |
884/840 (100.0%/95.0%) |
884/843 (100.0%/95.4%) |
882/835 (99.8%/94.5%) |
880/809 (99.5%/91.5%) |
880/804 (99.6%/91.0%) |
875/810 (99.0%/91.6%) |
| Halobacterium salinarum | 68.0 | 550 |
549/533 (99.8%/96.9%) |
549/525 (99.8%/95.5%) |
549/520 (99.8%/94.6%) |
548/510 (99.6%/92.7%) |
544/494 (98.9%/89.8%) |
549/478 (99.8%/86.9%) |
531/418 (96.6%/76.0%) |
| Natronomonas pharaonis | 63.4 | 321 |
320/314 (99.7%/97.8%) |
320/314 (99.7%/97.8%) |
320/313 (99.7%/97.5%) |
321/307 (100%/95.6%) |
314/300 (97.8%/93.5%) |
320/304 (99.7%/94.7%) |
315/265 (98.1%/82.6%) |
| Bacillus subtilis | 43.5 | 148 |
148/144 (100%/97.3%) |
148/145 (100.0%/98.0%) |
148/144 (100.0%/97.3%) |
147/145 (99.3%/98.0%) |
144/139 (97.3%/93.9%) |
144/140 (97.3%/94.6%) |
146/142 (98.7%/96.0%) |
| Aeropyrum pernix | 56.3 | 131 |
131/128 (100%/97.7%) |
131/127 (100.0%/97.0%) |
131/128 (100.0%/97.7%) |
130/123 (99.2%/93.9%) |
130/124 (99.2%/94.7%) |
130/121 (99.2%/92.4%) |
131/116 (100%/88.6%) |
| Synechocystis PCC6803 | 47.8 | 102 |
102/99 (100%/97.0%) |
102/98 (100%/96.1%) |
102/93 (100%/91.2%) |
102/92 (100%/90.2%) |
101/87 (99.0%/85.3%) |
102/84 (100%/82.4%) |
100/88 (98.0%/86.3%) |
| Pseudomonas aeruginosa | 66.6 | 122 |
118/116 (96.7%/95.1%) |
118/113 (96.7%/92.6%) |
118/115 (96.7%/94.3%) |
115/105 (94.3%/86.1%) |
122/112 (100%/91.8%) |
120/113 (98.4%/92.6%) |
117/113 (95.9%/92.6%) |
| Mycobacterium tuberculosis H37Rv | 65.6 | 62 |
62/58 (100%/93.6%) |
62/58 (100%/93.6%) |
62/57 (100%/91.9%) |
61/54 (98.4%/87.1%) |
62/58 (100%/93.6%) |
61/55 (98.4%/88.7%) |
60/56 (96.8%/90.3%) |
| Haemophilus influenzae | 38.2 | 67 |
67/66 (100%/98.5%) |
67/67 (100%/100%) |
67/67 (100%/100%) |
67/65 (100%/97.0%) |
67/67 (100%/100%) |
67/65 (100%/97.0%) |
66/65 (98.5%/97.0%) |
| Sulfolobus solfataricus | 35.8 | 56 |
56/51 (100%/91.1%) |
56/49 (100%/87.5%) |
56/49 (100%/87.5%) |
56/48 (100%/85.7%) |
56/51 (100%/91.1%) |
56/49 (100%/87.5%) |
56/50 (100%/89.3%) |
| All Genomes | --- | 2443 |
2437/2362 (99.8%/96.7%) |
2437/2336 (99.8%/95.6%) |
2437/2329 (99.8%/95.3%) |
2429/2284 (99.4%/93.5%) |
2420/2241 (99.1%/91.7%) |
2429/2213 (99.4%/90.6%) |
2397/2123 (98.1%/86.9%) |
