Systematic identification of stem-loop containing sequence families in bacterial genomes

BMC Genomics

Table 1 Sequence-based clustering of SLSs.

Division	Species	SLSs	Clusters	Clustered SLSs	Clustered SCRs
low-GC Firmicutes	Bacillus anthracis	65,220	4	105	38
	Bacillus halodurans	55,624	6	182	93
	Bacillus subtilis	56,622	2	32	16
	Clostridium perfringens	35,027	6	149	81
	Clostridium tetani	29,883	14	178	123
	Enterococcus faecalis	40,991	7	317	142
	Lactobacillus johnsonii	25,668	3	173	26
	Staphylococcus aureus	32,372	11	275	144
	Streptococcus pneumoniae	25,095	28	825	386
Mollicutes	Mycoplasma genitalium	8,953	1	21	8
	Mycoplasma pneumoniae	13,926	20	372	165
high-GC Firmicutes	Corynebacterium diphtheriae	54,254	9	282	120
	Mycobacterium leprae	83,094	29	1,721	537
	Mycobacterium tuberculosis	170,502	59	2,182	636
α-Proteobacteria	Brucella melitensis	69,899	11	399	219
	Rickettsia conorii	14,933	19	797	383
β-Proteobacteria	Bordetella bronchiseptica	214,459	26	2,009	470
	Bordetella parapertussis	188,237	30	1,513	518
	Bordetella pertussis	158,592	52	7,212	4,602
	Neisseria meningitidis	56,605	44	3,595	991
γ-Proteobacteria	Escherichia coli	86,339	12	1,152	431
	Haemophilus influenzae	25,055	3	39	25
	Pasteurella multocida	31,209	1	24	8
	Pseudomonas aeruginosa	206,492	9	526	129
	Pseudomonas putida	175,088	75	3,640	1,352
	Salmonella typhi	90,027	8	177	116
	Salmonella typhimurium	91,844	7	157	94
	Vibrio cholerae	45,824	7	250	122
	Yersinia pestis	78,372	20	600	279
TOTAL		2,230,206	523	28,904	12,254

BLAST-MCL clustering of SLSs identified, from a representative set of bacterial genomes, as described in Petrillo et al. [18]: only species with at least one cluster of a minimum of 7 elements are listed. For each species, the number of elements within the starting population, the number of clusters and the number of clustered SLSs are reported. The number of SLS containing regions (SCRs), obtained by fusing overlapping clustered SLSs, is also reported.

ISSN: 1471-2164