How can I find the frequency of the recognition sites found in the genome?

Question

[zpl015]

Hi all,

Given that the restriction enzymes are Pstl and Mspl, and their recognition sequences are CTGCA^G and C^CGG, respectively, I would like to find out how often these cut sites are found in a bird genome.

I found an R package called 'REDseq', which seems to do the job but requires GRanges objects as input. I only have a fasta file, and I am unsure how to convert the fasta file to a GRanges object.

Does anyone know to do this? Or if there are any other tools that do the job?

Thank you for your attention, and any help would be much appreciated!

Zoe

Answer 1

[GenoMax]

Not sure exactly what you are looking for but you can find the locations of restriction enzyme sites in your fasta file using restrict from EMOBSS. A web front end is available here: https://www.bioinformatics.nl/cgi-bin/emboss/restrict

[zpl015]

Thank you! This looks like what I need!