Evaluation of a microarray-hybridization based method applicable for discovery of single nucleotide polymorphisms (SNPs) in the Pseudomonas aeruginosa genome

Table 2 In silico comparison and comparative hybridization results for the two wbp gene clusters of PAO1

gene information			in silico analysis						comparative hybridization
			count of similarity classes^a
PAO1 locus ID	PA14 locus ID	gene name	ident.	SNP	mism.	absent	total	average sequence similarity	detected oligos^b	sensitivity^b
PA3141	PA14_23470	wbpM	54	7	4	5	70	0.97	12	0.75
PA3142*	absent		4	3	4	1	12	0.93	7	0.88
PA3143*	absent		4	4	8	3	19	0.90	11	0.73
PA3144*	absent		1	0	4	0	5	0.91	4	1.00
PA3145*	PA14_23460	wbpL	0	0	3	33	36	0.71	35	0.97
PA3146*	PA14_23450	wbpK	0	0	6	28	34	0.71	33	0.97
PA3147*	absent	wbpJ	0	0	6	37	43	0.72	43	1.00
PA3148*	absent	wbpI	0	0	7	30	37	0.74	37	1.00
PA3149*	absent	wbpH	0	0	6	33	39	0.72	39	1.00
PA3150*	absent	wbpG	0	0	3	36	39	0.70	39	1.00
PA3151*	absent	hisF2	0	0	3	24	27	0.69	26	0.96
PA3152*	absent	hisH2	0	0	1	21	22	0.70	22	1.00
PA3153*	absent	wzx	0	0	1	43	44	0.71	43	0.98
PA3154*	absent	wzy	0	0	1	45	46	0.70	46	1.00
PA3155*	absent	wbpE	0	0	5	33	38	0.72	38	1.00
PA3156*	absent	wbpD	0	0	4	17	21	0.72	20	0.95
PA3157*	absent		0	0	14	51	65	0.73	64	0.98
PA3158*	absent	wbpB	0	0	7	26	33	0.74	33	1.00
PA3159*	absent	wbpA	0	0	14	32	46	0.73	46	1.00
PA3160	PA14_23360	wzz	0	0	5	31	36	0.71	36	1.00
PA3161	PA14_23340	himD	8	1	1	0	10	0.99	1	0.50
PA5447	PA14_71910	wbpZ	35	4	1	0	40	0.99	5	1.00
PA5448	PA14_71920	wbpY	34	5	0	0	39	0.99	2	0.40
PA5449	PA14_71930	wbpX	40	8	1	0	49	0.99	4	0.44
PA5450	PA14_71940	wzt	40	5	0	0	45	1.00	3	0.60
PA5451	PA14_71960	wzm	24	5	0	0	29	0.99	3	0.60
PA5452	PA14_71970	wbpW	42	6	1	0	49	0.99	4	0.57

ISSN: 1471-2164