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.
Bsseq: A Bioconductor (R) package that offers a suite of tools for analyzing and visualizing your very own WGBS data towards your goal of identifying differentially methylated regions (DMRs).
https://bioconductor.org/packages/release/bioc/html/bsseq.html
You can use
BiQ Analyzer
http://biq-analyzer.bioinf.mpi-inf.mpg.de/download.php
I think BiQ might be really useful. Working with restriction enzymes, have you also tried ApE software?
http://biq-analyzer.bioinf.mpi-inf.mpg.de/download.php
you can also Sanger sequence your product for SNP.
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