Wavelet to predict bacterial ori and ter: a tendency towards a physical balance

Song, Jiuzhou; Ware, Antony; Liu, Shu-Lin

doi:10.1186/1471-2164-4-17

BMC Genomics

Table 1 Predicted positions of ori and ter of sequenced bacterial chromosomes

From: Wavelet to predict bacterial ori and ter: a tendency towards a physical balance

			Predicted		Reported		*ori-ter* ^d	Quality
			Position ^b		Position^c		Degree
Bacterial strain	G.I.^a	Genome size (bp)	ori	ter	ori	ter		Keto	Purine
Bacillus halodurans C-125	BA000004	4202353	3462	2062112	N/A	N/A	174	Weak	Strong
Bacillus subtilis	AL009126	4214810	359	1941675	1	2017000	169	Strong	Strong
Borrelia burgdorferi	AE000783	910725	458751	910649	460000	N/A	179	strong	Weak
Campylobacter jejuni	AL11168	1641481	1607245	829145	N/A	N/A	189	Strong	Weak
Caulobacter crescentus	AE005673	4016947	18744	1922444	1	N/A	171	Strong	Weak
Chlamydia muridarum	AE002160	1069411	311	520681	N/A	N/A	176	Strong	Strong
Chlamydia trachomatis	AE001273	1042519	720352	201311	N/A	N/A	181	Strong	Strong
Chlamydophila pneumoniae AR39	AE002161	1229853	349	622737	N/A	N/A	183	Strong	Weak
Chlamydophila pneumoniae CWL029	AE001363	1230230	841233	218525	N/A	N/A	177	Strong	Weak
Chlamydophila pneumoniae J138	BA000008	1228267	840884	218478	N/A	N/A	177	Strong	Weak
Escherichia coli K12	U00096	4639221	3921168	1606253	3923000	1603000	180	Strong	Strong
Escherichia coli O157-H7 EDL933	AE005174	5528445	4786037	1974813	4788169	1102902	183	Strong	Strong
Escherichia coli O157-H7 Sakai-VT2	BA000007	5498450	4716984	2113730	4719188	1414737	189	Strong	Strong
Haemophilus influenzae	L42023	1830138	616817	1475181	N/A	1518000	169	Strong	Weak
Helicobacter pylori 26695	AE000511	1667867	1589717	683947	N/A	N/A	165	Strong	Weak
Helicobacter pylori J99	AE001349	1643831	142182	896905	N/A	N/A	166	Strong	Weak
Lactococcus lactis	AE005167	2365589	26262	1293666	N/A	N/A	193	Weak	Strong
Mesorhizobium loti	NC_002678	7036074	3944132	148671	N/A	N/A	166	Strong	Weak
Mycobacterium leprae	AL450380	3268203	1833	1707503	N/A	N/A	188	Strong	Weak
Mycobacterium tuberculosis	AL123456	4403836	1784	2084147	N/A	N/A	171	Strong	Weak
Mycobacterium tuberculosis H37R	AE000516	4411529	1784	2086919	N/A	N/A	171	Strong	Weak
Mycoplasma genitalium	NC_000908	580074	349919	95535	N/A	N/A	202	Weak	Strong
Neisseria meningitidis MC58	AE002098	2272351	13698	1241287	N/A	N/A	195	Strong	Strong
Neisseria meningitidis Z2491	AL157959	2184406	247606	1307356	N/A	N/A	175	Strong	Strong
Pseudomonas aeruginosa	AE004091	6264403	5852734	2586738	N/A	N/A	172	Strong	Strong
Rickettsia conorii	NC_003103	1268823	1243683	607194	N/A	N/A	180	Strong	Weak
Salmonella typhi CT18	AE006469	4809037	3765414	1486510	3765000	1437000	189	Strong	Strong
Salmonella typhimurium LT2	BA000017	4857432	4083786	1635863	N/A	N/A	178	Strong	Strong
Sinorhizobium meliloti	NC_002745	3654135	3476969	1718933	N/A	N/A	186	Strong	Weak
Staphylococcus aureus Mu50	AE004092	2878040	1749987	361672	N/A	N/A	186	Weak	Strong
Staphylococcus aureus N315	AE006641	2813695	1750052	349713	N/A	N/A	181	Weak	Strong
Streptococcus pneumoniae TIGR4	AB001339	2160837	2504	1065319	N/A	N/A	177	Weak	Strong
Streptococcus pyogenes	AE000512	1852441	12348	963378	N/A	N/A	185	Weak	Strong
Treponema pallidum	AE000520	1138011	3306	556361	N/A	N/A	175	Strong	Weak
Ureaplasma urealyticum	NC_002162	751719	40119	411530	N/A	N/A	178	Weak	Strong
Vibrio cholerae	AE003852	2961149	2959988	1573399	N/A	N/A	192	Strong	Strong

Note: ^a, G.I., GenInfo Identifiers. ^b, Predicted position, minimum (ori) and maximum (ter), see details in text. ^c, Reported position, oriC and terC positions reported by the authors. ^d, ori-ter (Degree), physical distance of the predicted ori and ter in degree clockwise from ori to ter. ^e, Quality, keto and purine excesses with minimum and maximum clearly (strong) or not clearly (weak) shown on the curves, see the text and Figures 5, 6 and 7.

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ISSN: 1471-2164

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