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 pretrained 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 Rvalue threshold of R = 2. 

Larsen and Krogh BMC Bioinformatics 2003 4:21 doi:10.1186/14712105421 