[Bioperl-l] Pattern finding and mismatches

Michael Thon mthon at tamu.edu
Thu Aug 3 21:11:08 EDT 2006

Hi Nick - I don't know if you can do this directly with bioperl, but  
I think the EMBOSS program fuzznuc will do what you want.


On Aug 3, 2006, at 11:53 AM, staffa wrote:

> I have seen bioperl modules for finding restriction sites and  
> fragment lengths, and one could create his own pattern to search for,
> but is there anything like GCG's findpatterns that would allow me  
> to search for a 21bp pattern but allow 2 mismatches anywhere?
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
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> National Institutes of Health
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