Hello,

I have a custom Affy Genechip that was designed using a draft version of a bacterial genome. We now have the finished version of the genome sequence available, so I would like to re-annotate the microarray probes to reflect the new genome sequence and gene numbering system. 

This problem appears to be something that many groups deal with on a regular basis, and I know that Affy constantly updates its annotation. 

Therefore, I was wondering if anyone could guide me in how I can go about re-annotating my array probes? Perhaps you have a pipeline that would be easily adapted to my probes and genome sequence? I know the basic sequence of events: map probes to new gene set->take list of exact matches->re-group probes->create CDF, but I don't know how to actually achieve these steps. 

Thank you for any help or points you can provide. 

Ariel Grostern

post-doctoral researcher
Alvarez-Cohen Lab
Civil and Environmental Engineering
UC Berkeley
arielDOTgrosternATberkeleyDOTedu

	[[alternative HTML version deleted]]

