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 stucked on the second step. I cant decide. to the oligonucleotide probes that willl 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 experinced helpers??????