Table 4

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

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


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.

Larsen and Krogh BMC Bioinformatics 2003 4:21   doi:10.1186/1471-2105-4-21

Open Data