[Bioperl-l] Pattern finding and mismatches

Brian Osborne osborne1 at optonline.net
Fri Aug 4 19:56:15 EDT 2006


Michael and Nick,

This question is also addressed in the FAQ:

http://www.bioperl.org/wiki/FAQ#How_do_I_do_motif_searches_with_BioPerl.3F_C
an_I_do_.22find_all_sequences_that_are_75.25_identical.22_to_a_given_motif.3
F

Brian O.


On 8/3/06 9:11 PM, "Michael Thon" <mthon at tamu.edu> wrote:

> 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.
> emboss.sourceforge.net
> 
> M
> 
> 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
>> NIEHS Information Technology Support Services Contract
>> (Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
>> National Institute of Environmental Health Sciences
>> National Institutes of Health
>> Research Triangle Park, North Carolina
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> 
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