Hello,

I am working with SNP genotyping by PCR-RFLP method. When I put the FASTA sequence of my target region in the NEB cutter to know the relevant cut site of the restriction enzymes, it shows cleavage affected by cpg methylation or cleavage affected by other methylation in case of some enzymes. Should I use those enzyme for genotyping my SNP locus?? I think if there is any methylation in DNA then restriction enzymes will not cut that site. Then how can I determine the polymorphic allele?? Is there any in silico method to check DNA methylation before doing RFLP??? Please suggest.