Table 4 A sample of classification rules at the species level extracted by the DMB software. f(W) represents the relative frequency of substring W in a genome, multiplied by 105 for readability
From: LAF: Logic Alignment Free and its application to bacterial genomes classification
A. baumannii | f(GTAC)≥229.10∧f(TGCA)≥515.63 |
B. cereus | 384.04≤f(CTCA)<490.11∧819.04≤f(TCCA)<875.80 |
B. animalis | 762.28≤f(TCCA)<819.04∧469.35≤f(TGCA)<515.63 |
B. longum | f(GTAC)≥229.10∧330.52≤f(TGCA)<376.80 |
B. aphidicola | 57.77≤f(AGGC)<182.81 |
C. jejuni | 490.11≤f(CTCA)<596.17∧353.97≤f(CTGA)<451.85 |
C. trachomatis | 305.55≤f(GGAC)<393.10∧875.80≤f(TCCA)<932.56 |
C. botulinum | 371.77≤f(ACTC)<434.37∧112.00≤f(GCAC)<261.71 |
C. diphtheriae | 819.04≤f(TCCA)<875.80∧423.07≤f(TGCA)<469.35 |
C. pseudotuberculosis | 875.80≤f(TCCA)<932.56∧423.07≤f(TGCA)<469.35 |
E. coli | 710.86≤f(GCAC)<860.58∧415.84≤f(GCTA)<525.98 |
F. tularensis | 592.00≤f(TCCA)<648.76∧330.52≤f(TGCA)<376.80 |
H. influenzae | 549.73≤f(CTGA)<647.60∧130.47≤f(GGAC)<218.01 |
H. pylori | 5.56≤f(GTAC)<42.82 |
L. monocytogenes | 411.43≤f(GCAC)<561.15∧305.55≤f(GGAC)<393.10 |
M. tuberculosis | 649.71≤f(ATCA)<772.78 |
N. meningitidis | 590.29≤f(GATA)<754.27∧376.80≤f(TGCA)<423.07 |
P. marinus | (f(AGGA)<602.46∨f(AGGA)≥706.28)∧f(GCTA)<856.37 |
∧117.33≤f(GTAC)<154.58 | |
S. enterica | 525.98≤f(GCTA)<636.11∧393.10≤f(GGAC)<480.64 |
S. aureus | 1082.23≤f(GATA)<1246.22∧f(GTAC)≥229.10 |
S. pneumoniae | 393.10≤f(GGAC)<480.64∧154.58≤f(GTAC)<191.84 |
S. pyogenes | 596.06≤f(AGTA)<733.86∧1082.23≤f(GATA)<1246.22 |
S. suis | 918.25≤f(GATA)<1082.23∧330.52≤f(TGCA)<376.80 |
S. islandicus | 218.01≤f(GGAC)<305.55∧284.24≤f(TGCA)<330.52 |
Y. pestis | 596.17≤f(CTCA)<702.24∧f(CTGA)≥941.24 |