Finding structural variations in bacteria

Question

[mmart12]

Hello,
I've got a couple of bacterial genomes and I'd like to design two different PCR tests to discriminate each of them from all the other members of the species. I assembled the genomes with SPADEs and I was wondering whether there is an easy way to find genes with different length, which would be the best solution for the PCR design.

Thanks a lot

Answer 1

[h.mon]

Align your genomes (e.g. with Mauve) and then search for larger indels. Inversions could potentially be good targets.

Answer 2

[Antonio R. Franco]

Mauve will compare both sequences, but there is a more convenient utility that will tell you exactly the ranges of sequence similarity.Take a look to the VISTA genome tools