Sorry if this is a bit of a silly question, but I'm looking for a few opinions on my methods....

I have a core genome alignment of 50 isolates, from which I have detected multiple regions of recombination (either in a single isolate or in multiple).

I would like to analyse the genes that are affected by these recombination events, and am wondering the best method?

So far I have used two methods; 1) Blast2go whereby I have blasted each recombining region. This has worked for most of my recombining segments but not all - a few segments >10,000bp have come back with no hits 2) As I have annotated my core genome, I have used the coordinates of the recombining regions to determine which genes are contained within these segments, but obviously for large recombining segments I get a lot of hits.

Which method is most appropriate?