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Table 4 Comparison with Genbank Annotations

From: Prodigal: prokaryotic gene recognition and translation initiation site identification

Organism Genbank Genes with no Joins Prodigal 1.20 Prodigal 1.20+TiCo Prodigal 1.20+TriTisa GenemarkHMM 2.6 Glimmer 3.02 EasyGene 1.2 MED 2.0
Escherichia coli K12 4268 4118/3823 (96.5%/89.6%) 4118/3779 (96.5%/88.5%) 4118/3778 (96.5%/88.5%) 4122/3685 (96.6%/86.3%) 4076/3563 (95.5%/83.5%) 3977/3565 (93.2%/83.5%) 4102/3711 (96.1%/86.9%)
Halobacterium salinarum 2110 2062/1857 (97.7%/88.0%) 2062/1809 (97.7%/85.7%) 2061/1790 (97.6%/84.8%) 2042/1676 (96.7%/79.4%) 2054/1609 (97.3%/76.2%) 2018/1692 (95.6%/80.2%) 2008/1469 (95.1%/69.6%)
Natronomonas pharaonis 2661 2630/2398 (98.8%/90.1%) 2630/2358 (98.8%/88.6%) 2630/2348 (98.8%/88.2%) 2624/2251 (98.6%/84.6%) 2622/2220 (98.5%/83.4%) 2548/2271 (95.7%/85.3%) 2586/1953 (97.2%/73.4%)
Bacillus subtilis 4174 4113/3705 (98.5%/88.8%) 4113/3678 (98.5%/88.1%) 4113/3679 (98.5%/88.1%) 4136/3713 (99.1%/89.0%) 4102/3569 (98.3%/85.5%) 3977/3578 (95.3%/85.7%) 4127/3596 (98.9%/86.2%)
Aeropyrum pernix 1699 1670/1430 (98.3%/84.2%) 1670/1363 (98.3%/80.2%) 1670/1353 (98.3%/79.6%) 1672/1364 (98.4%/80.3%) 1671/1317 (98.4%/77.5%) 1652/1389 (97.2%/81.8%) 1689/1309 (99.4%/77.1%)
Synechocystis PCC6803 3171 3146/2587 (99.2%/81.6%) 3146/2364 (99.2%/74.6%) 3146/2447 (99.2%/77.2%) 3124/2337 (98.5%/73.7%) 3123/2236 (98.5%/70.5%) 3053/2288 (96.3%/72.2%) 3126/2192 (98.6%/69.1%)
Pseudomonas aeruginosa 5565 5514/5038 (99.1%/90.5%) 5514/4885 (99.1%/87.8%) 5514/4821 (99.1%/86.6%) 5484/4698 (98.5%/84.4%) 5491/4705 (98.7%/84.5%) 5522/4761 (99.2%/85.5%) 5292/4539 (95.1%/81.6%)
  1. Table 4 shows the performance of gene-finding algorithms on seven Genbank files. 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. It should be noted that Genbank genes are not experimentally verified; this table is just meant to provide a snapshot of performance over entire genomes.