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Finding structural variations in bacteria

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

snp alignment gene
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updated by Antonio R. Franco Antonio R. Franco • written by mmart12 • mmart12

2 answers

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

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written by h.mon h.mon

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

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written by Antonio R. Franco Antonio R. Franco

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