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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%) |
