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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%)
  1. Table 3 shows the performance of gene-finding algorithms on ten sets of experimentally verified genes with experimentally verified translation initiation sites. The first number in each entry indicates the number of 3' ends of genes correctly identified. The second number in each entry indicates the number of 5'+3' ends (genes and their correct starts) exactly identified. Beneath these numbers are % representations for each of those values. The final row shows the performance over the entire set of organisms.