[Bioperl-l] Re: A question about Bioperl module

Steve Chervitz sac at portal.open-bio.org
Fri Jul 1 16:56:07 EDT 2005

Hi Gao Zhang,

No, SeqPattern cannot generate random motifs, and I'm not aware of any
modules in Bioperl than can do so (anyone else know?). The String::Random
module might be sufficient for your needs:



> From: <gaozhang at mail.med.upenn.edu>
> Date: Thu, 30 Jun 2005 12:03:40 -0400
> To: <sac at bioperl.org>
> Subject: A question about Bioperl module
> Dear Steve Chervitz,
> Hi! This is Gao Zhang, a Ph.D student in Graduate Group
> in Genomics and Computational Biology at University of
> Pennsylvinia. I am working on discovery of motifs using
> DNA sequence and find Bio::Tools::SeqPattern module might be
> helpful for me.
> My question is that whether it has any module which is
> able to generate a random motif of width w like 8. In this motif,
> each position will have a dominant letter with probability around
> x like 0.91.
> Thank you very much and look forward to your reply!
> Best Regards,
>    Gao Zhang

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