Hello, I was reading this paper and was wondering.
For some simple organisms, like Mycobacterium bovis, Mycobacterium tuberculosis, there is a great number of whole sequences in genbank for example.
Is it possible to, white a whole genome sequence, type the organism?
If I'm not understanding it wrong, the Restriction fragment length polymorphism (RFLP) typing consist of the amplification of an area of the DNA, which, if we know the primers, we could simple get on the whole genome right?
Then cut it with a RFLP, which cut the sequence in a specific sequence, for example, ACCT, so every ACCT on the sequence will make a cut, transforming the sequence extracted on the step above into many sequences of various lengths. And them compare the lengths with a reference, the lengths are black thinks saw in figure 2 on the paper of the link right? So we known that are sequences of x bases, sequences of y bases, and comparing these numbers with the reference we give a name to the organism, a type?
If I'm not totally misinterpreting, are this procedure possible and implemented in some language, python or R with Bioconductor? The procedure to take a whole genome and type it with RFLP vs a reference? Also can someone suggest more literature about this?
I think you're describing RFLP fingerprinting, where if we run the same RFLP assay on two samples we can see if they're the same individual. It won;t be perfectly the same, but for the most part it works between real samples. The reference genomes aren't really so accurate, so you should try a known sample to compare against.