Pathogen Identification via Oligo-Array

Question

[mr.donmez.emre]

Dear All

For my phd THESİS;

I designed microarray assay for detecting pathogens(15 pathogen including gram + and gram -) from blood cultures and need suggestions;

I have two steps on the experiment.

1. Amplification of 300bp amplicon of gyrB gene (by using only 1 primer pair/ including degenerated mix bases of course) of pathogens DNA isolated from positive cultures
2. Using fluoresecence microarray analyzer for detecting the hybridized probes.

I got stuck on the second step. I can't decide. to the oligonucleotide probes that will be attached to the slide :(

I mean, I can select the probes manually ( 20-25bp) and confirm them by my own EYEs ON THE ALIGNMENT FILES. But I would like to check via confirmational softwares for more details on analytical points.

Any experienced helpers?

Thanks

Looking forward

Emre