Comparing intergenic regions and their flanking genes

[Barbara MacGregor]

Hi,

There is probably a way to do this and I'm just not seeing it. I have some conserved intergenic sequences and would like to look at their flanking genes, ideally with something like the "Gene Neighborhoods" maps. Is there a way to get from a list of intergenic blastn hits to a set of gene maps, or failing that to a list of flanking genes? I have hundreds of examples, in several genomes, so calling up the contigs one by one by one is not really an option for this lifetime.

Bonus points for then transferring this information to an Arb file of the aligned intergenic regions...

Thanks,

Barbara