In silico microarray probe design for diagnosis of multiple pathogens

BMC Genomics

Table 5 Evaluation of in silico (design) probes against hybridization results with R^U= 1.0 and R^L= 0.5 for five categories of probes

Category (targets)	In silico	Experimental
		Class A	Class B	Class C
I (B. mallei ATCC 23344)	0	0 (0%)	0 (0%)	0 (0%)
II (B. mallei NCTC 10229)	2	0 (0%)	2 (100%)	0 (0%)
III (B. pseudomallei K96243)	523	420 (80%)	53 (10%)	50 (10%)
IV (B. mallei ATCC 23344 and B. mallei NCTC 10229)	21	17 (81%)	2 (10%)	2 (10%)
V (B. mallei ATCC 23344, B. mallei NCTC 10229 and B. pseudomallei K96243)	431	184 (43%)	12 (3%)	236 (55%)

Probes that behave as expected are categorized as Class A; i.e., these probes have normalized hybridization intensity greater than R^Uwith intended targets and less than R^Lwith non-targets. Class B probes have normalized hybridization intensity greater than R^Lwith non-targets, and Class C probes have normalized hybridization intensity less than R^Uwith the intended targets.

ISSN: 1471-2164