Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs

BMC Bioinformatics

Table 1 Analysis of characterized promoter sequences in ten bacterial genomes.

						Organism-specialized matrices			General matrix
Organism	GC	Prom.	IRs	Nt	Spacing	Sensitivity	FP/100 nt	Name	Sensitivity	FP/100 nt
E. coli	50.8%	377	335	117238	16–20	42.4%	1.13	229794169	31.0%	1.09
B. subtilis	43.5%	148	142	43446	16–20	56.8%	0.99	113362653	50.0%	0.93
C. glutamicum	53.8%	34	33	13572	16–20	29.4%	1.36	223574489	14.7%	1.36
M. pneumoniae	40.0%	30	27	7662	15–19	43.3%	1.08	235984178	30.0%	1.07
M. tuberculosis	65.6%	28	25	7812	16–20	57.1%	0.74	223574908	50.0%	0.84
S. coelicolor	72.1%	17	17	5756	16–20	58.8%	1.42	248361134	47.1%	1.27
H. pylori	38.9%	17	16	4725	19–23	47.1%	0.53	91939249	35.3%	0.70
C. jejuni	30.5%	14	14	2872	16–20	42.9%	0.84	107109675	35.7%	0.77
B. japonicum	64.1%	11	11	4229	16–20	90.9%	0.73	192892765	90.9%	0.97
S. aureus	32.9%	8	5	2206	16–20	37.5%	0.59	24624174	37.5%	1.13

For each organism, the GC content, the number of gathered characterized promoter sequences, the number of distinct IRs containing these promoters, the total number of nt in these IRs, and the allowed spacing between hexanucleotide pairs are indicated. The sensitivity and FP rate obtained with the best synthetic matrix (organism-specialized) and the general matrix are also shown.

ISSN: 1471-2105