9.3 years ago by
It is not quite clear from your question, but I assume that what you are talking about is genotyping of a particular species of bacteria. Since they have been genotyped for 90 SNPs, my guess would be that these SNPs were not picked at random. Most likely, it is a set of SNPs that is commonly used for distinguishing between different strains of the bacterium in question.
My guess is thus that would you should really look for is a genotyping database of strains of the particular species that you are working on. Most likely many, many more different strains have been genotyped than have been fully sequenced. If you find such a database, the analysis that you talk about would be a simple matter of comparing the SNPs from your samples to the reference samples in the database.
Unless you tell us which species it is you are working on, I don't think we will be able to help you much further.