Need to identify conserved exons among 3 genomes

[kmkocot]

Hi all,

I want to identify conserved exons present in 3 eukaryotic genomes. I have the complete genomic scaffolds, predicted transcripts, and predicted proteins. My goal is to design degenerate primers that will amplify relatively conserved exons for a phylogenetic study.

Can anyone suggest a good strategy for doing this?

Best,
Kevin

[JackieBadger]

I am assuming you want conserved priming regions within these exons which span some variability between species?
I would BLAST your genomes against each other to reveal similar transcripts and then just design primers from the alignment. You can use BFAST (a modified fast version of BLAT) to do this. BLASTing whole scaffolds may take a long time, BFAST is designed so to speed up the process greatly.
Its similar to the process of designing EPIC primers....for this you would align well annotated genomes (so to ID spice sites) (http://www.biomedcentral.com/1471-2148/10/90).... if you wanted to align your transcripts to genomes using BLAT this would take into consideration predicted splice sites (if you already do not have this info)