Biomarker Identification with Whole Genome Sequence Alignment

Question

[OPH]

Hello, I am attempting to identify a biomarker target to identify a particular bacteria using PCR because the current available gene targets do not discriminate the bacteria I want to identify from closely related strains. How should I go about this. I was thinking of using whole genome sequence alignment software and aligning whole genome sequences for the particular bacteria I want to identify and then aligning this to the genome of the bacteria I don't want to identify, so as to identify possible target regions. Any advice?

[mikhail.shugay]

Check this out: http://bioinformatics.oxfordjournals.org/content/27/3/334.long. The paper claims that the tool is suited for homologous genomes and provide sequence conservation as output. So you could manually select some of the least-conserved genes.