[Bioperl-l] getting patterns consensus

[Stefan Kirov]

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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e-mail: skirov at utk.edu
sao at ornl.gov

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