[Bioperl-l] getting patterns consensus
skirov at utk.edu
Fri Jul 22 13:39:07 EDT 2005
Thanks, but actually the module is written by Aaaron Mackay, so I guess
your gratitude goes to him :-) .
> 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
> 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.
>>>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:
>>>Bioperl-l mailing list
>>>Bioperl-l at portal.open-bio.org <mailto: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
e-mail: skirov at utk.edu
sao at ornl.gov
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