Tool for Identifying Restriction Sites at IUPAC SNP sites?

[brachysclereid]

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!

[maasha]

Hello,


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

http://code.google.com/p/biopieces/wiki/rescan_seq

and possibly

http://code.google.com/p/biopieces/wiki/digest_seq

Martin

[brachysclereid]

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.

[maubp]

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.

[maasha]

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

[maubp]

What do you mean by this? Biopieces are meant to be easy!

That was partly in reference to:

... 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.