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

Table 6 Signal ratios of SNPs are influenced by interaction of neighboring nucleotides

neighboring nucleotides	abundance	median signal ratio	sensitivity^b
W-W^a	3223	-0.77	63.2%
W-S or S-W	14599	-0.54	52.5%
S-S	11123	-0.39	42.7%
marginal^c	2640	0.07	2.2%
	31585	-0.43	45.9%

^a W – IUPAC format bases A, T showing weak interaction, S – IUPAC for G, C showing strong interaction.
^b determined for D_th= -0.5.
^c SNPs in the marginal position 1 or 25 that don't have two neighboring nucleotides (see also Figure 6).

ISSN: 1471-2164