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  • Tool for Identifying Restriction Sites at IUPAC SNP sites?

    Does anyone know of a tool that can be used to identify & report restriction sites only at IUPAC ambiguity codes? I am looking for something that can process entire FASTA files(with many scaffolds) and report coordinates and enzymes.

    Thanks!

  • #2
    Hello,


    I am not quite sure what you are after, but I think Biopieces (www.biopieces.org) might help you. Have a look at



    and possibly




    Martin

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    • #3
      Identifying restriction sites using Biopieces

      Thanks Martin. The Biopiece: digest_seq module looks like it might do the trick. It looks like it might take a bit of work to get all the dependencies installed, but it will probably be worth the effort. My project is rather basic. I am just trying to find restriction enzymes that cut only at SNP sites that are heterozygous in a single individual. These sites are marked with IUPAC ambiguity codes in my sequence.

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      • #4
        Can you program? If so a Perl/Python/... script might be easier, and the BioPerl/Biopython/... libraries will probably all include some sort of restriction digest support to help you.

        Comment


        • #5
          Originally posted by maubp View Post
          a Perl/Python/... script might be easier, and the BioPerl/Biopython/...
          What do you mean by this? Biopieces are meant to be easy!


          Cheers,


          Martin

          Comment


          • #6
            Originally posted by maasha View Post
            What do you mean by this? Biopieces are meant to be easy!
            That was partly in reference to:
            Originally posted by brachysclereid View Post
            ... It looks like it might take a bit of work to get all the dependencies installed, but it will probably be worth the effort...
            But also if you are familiar with a scripting language, that may be easier than learning a new suite of command line tools. Different people find different things easier - I was not meaning to suggest Biopieces is hard.

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