inexpensive method to detect SNPs in entire bacterial genomes

Question

[sapuizait]

Dear all

Does sb know of a cheap method to detect if there are any SNPs between two bacterial genomes? I have to check thousands of clones for SNPs - I only need to find out if there are any SNPs, not to map them - and WGS is not a feasible option due to cost. I was wondering if there is a molecular method that could tell me if there is a difference between two clonal strains and if yes, then do WGS to map the SNPs. From the top of my head I was thinking sth like MDA-amplification and RFLP but I am not sure how feasible it is or if there is a better method. I am aware that there is a real-time PCR option as well but I am not interested in checking a few marker genes but rather entire bacterial genomes.

Thanks!

Answer 1

[Mensur Dlakic]

This really isn't a bioinformatics question.

If I understand correctly what you want: a cheap method that operates on a large scale, because you are interested in SNPs across the whole genome, plus you have thousands of colonies. Assuming that you want this experimental approach to be reliable, I am pretty certain that no such method exists.

There is a saying in food industry that is very applicable to all other work domains: