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Table 4 Specificity, sensitivity and precision estimates for M. tuberculosis, H. pylori J99 and B. subtilis.

From: EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance

M. tuberculosis
Data set EasyGene GmS Frame
A'-% found 96.7 97.2 96.0
A'-% exact 89.1 80.9 87.9
B'-% found 96.8 97.1 96.3
T-% found 96.9(96.6) 97.3 96.4
Genome 3749 3983 4341
zero order 0 - 8
first order 3 - 2
third order 2 - 12
shadows 1 0 1
H. pylori J99
Data set EasyGene GmS Frame
A'-% found 99.2 99.2 99.2
A'-% exact 97.5 95.7 96.7
B'-% found 100 99.6 98.9
T-% found 99.7(98.8) 99.5 99.1
Genome 1491 1518 1479
zero order 2 1479 2
first order 1 336 2
third order 0 403 0
shadows 2 0 0
B. subtilis
Data set EasyGene GmS Frame
A'-% found 99.3 98.1 98.8
A'-% exacts 94.8 94.1 93.3
B'-% found 99.2 99.0 98.2
T-% found 99.3(99.2) 99.0 98.4
Genome 4083 4221 4006
zero order 1 675 0
first order 2 457 0
third order 1 813 2
shadows 0 0 0
  1. Genes found exactly and partially for different gene finders and sets of high confidence genes in M. tuberculosis, H. pylori J99 and B. subtilis, where the number of annotated genes is 3918, 1491 and 4100 respectively. There are no pre-trained GeneMarkS models for M. tuberculosis, so it was not possible to obtain a false positive estimate for this organism. All values listed for EasyGene are based on an R-value threshold of R = 2.