[Bioperl-l] getting patterns consensus

Stefan Kirov skirov at utk.edu
Fri Jul 22 10:59:40 EDT 2005

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.

khoueiry wrote:

>Hi all,
>Let's admit that I have the following pattern : 
>Is there a bioperl method or a fine/fast perl way to get all the
>consensus relative to that pattern:
> (i.e)
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

"And the wars go on with brainwashed pride
For the love of God and our human rights
And all these things are swept aside"

More information about the Bioperl-l mailing list