How to find conserved regions in a genome

Question

[Nicolas]

Hello!

I would like to know it there is any tool to find conserved regions within a set of genomes. Basically I have to design some primers to detect a patoghen, and I would like to target a region that is conserved among different strains of this pathogen.

I was thinking that I could download the whole genome of each strain, align them and find which regions are more conserved. Is there any tool to do this?

Thank you!

Answer 1

[Pierre Lindenbaum]

http://compgen.cshl.edu/phast/

[Nicolas]

I'm going to take a look at it. Thank you!