[Bioperl-l] getting patterns consensus

[Stefan Kirov]

Pierre,
Thanks, but actually the module is written by Aaaron Mackay, so I guess 
your gratitude goes to him :-) .
Stefan

khoueiry wrote:

> Thanks,
>
> Kirov, Your method did exactly what I need. brian, no I  don't think 
> that Bio::Tools::SeqPattern resolve the prob unless  something's 
> missing me.
>
> Thanks again
>
> Pierre
>
> Le vendredi 22 juillet 2005 à 10:59 -0400, Stefan Kirov a écrit :
>
>>Yes. Look at Bio::Tools::IUPAC. Create the Bio::Seq object, using IUPAC 
>>coding for ambiguous nucleotides (see the documentation) and then create 
>>the IUPAC object based on the seq one. Then use next_seq method- it will 
>>give you exactly what you need.
>>Stefan
>>
>>khoueiry wrote:
>>
>>>Hi all,
>>>
>>>Let's admit that I have the following pattern : 
>>>
>>>$PAT = A[AT]GAT[CT]A
>>>
>>>Is there a bioperl method or a fine/fast perl way to get all the
>>>consensus relative to that pattern:
>>> (i.e)
>>>
>>>AAGATCA
>>>AAGATTA
>>>ATGATCA
>>>ATGATTA
>>>
>>>Thanks
>>>
>>>pierre
>>>
>>>
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>>>  
>>>
>>
>>    
>>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
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