Schematic representation of StaphChip probe selection. All ORFs of N315 were loaded into ArrayDesigner™ (a) to select oligonucleotides according to their thermodynamical properties (Step A). The 417,776 N315-derived probes were filtered for target specificity using BLAST against N315 genome (Step B). Each probe should recognize a single target yielding a defined signal intensity threshold, i.e. outside the green box (b), otherwise it is rejected (c). During Step C, all accepted probes are aligned against heterologous S. aureus genomes (i.e. Mu50 or COL) to annotate probes common to the other genomes (d, e). Each probe should recognize a single target yielding a defined signal intensity threshold, i.e. inside the red box (d), with no other signals outside the green box; otherwise it is ignored (e). The process is repeated from Step A to C with the two other strain databases. Final selection by spreadsheet analysis (Step D) yielded a total number of 5,427 probes hybridizing with one or more S. aureus genomes.