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Old 02-07-2011, 12:28 PM   #1
brachysclereid
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Default 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!
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Old 02-08-2011, 01:11 AM   #2
maasha
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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
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Old 02-08-2011, 07:37 AM   #3
brachysclereid
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Default 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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Old 02-08-2011, 09:16 AM   #4
maubp
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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.
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Old 02-08-2011, 09:38 AM   #5
maasha
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Quote:
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
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Old 02-09-2011, 01:58 AM   #6
maubp
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Quote:
Originally Posted by maasha View Post
What do you mean by this? Biopieces are meant to be easy!
That was partly in reference to:
Quote:
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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