Table 5

Number of Genes Predicted By Each Method

Organism

Genbank

EasyGene 1.2

Prodigal 1.20

GenemarkHMM 2.6

Glimmer 3.02

MED 2.0


Escherichia coli K12

4321 (1.00)

4099 (0.95)

4305 (1.00)

4378 (1.01)

4476 (1.04)

4811 (1.11)


Halobacterium salinarum

2110 (1.00)

2097 (0.99)

2101 (1.00)

2085 (0.99)

2141 (1.01)

2385 (1.13)


Natronomonas pharaonis

2661 (1.00)

2587 (0.97)

2678 (1.01)

2685 (1.01)

2720 (1.02)

3111 (1.17)


Bacillus subtilis

4177 (1.00)

4019 (0.96)

4224 (1.01)

4354 (1.04)

4429 (1.06)

4601 (1.10)


Aeropyrum pernix

1700 (1.00)

1686 (0.99)

1717 (1.01)

1738 (1.02)

1789 (1.05)

2419 (1.42)


Synechocystis PCC6803

3172 (1.00)

3089 (0.97)

3306 (1.04)

3462 (1.09)

3677 (1.16)

3778 (1.19)


Pseudomonas aeruginosa

5566 (1.00)

5910 (1.06)

5679 (1.02)

5712 (1.03)

5878 (1.06)

6709 (1.21)


Table 5 shows the number of genes predicted by each method on seven Genbank files. The Genbank column indicates the number of genes in the Genbank file. The number in parentheses indicates the number of predicted genes divided by the number of genes in the Genbank file, e.g. 1.10 indicates 10% more genes predicted than the Genbank file.

Hyatt et al. BMC Bioinformatics 2010 11:119   doi:10.1186/1471-2105-11-119

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