[Bioperl-l] getting patterns consensus

[khoueiry]

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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> >  
> >
>