[Bioperl-l] MEME parsing
skirov at utk.edu
Tue Nov 9 15:33:13 EST 2004
You can take a look at Bio::Matrix::PSM::IO... Are you looking into DNA
or protein? By the way I don't know if you remember that part of my
talk, but our pipeline does exactly that- runs meme in batch mode. We
have set up a database to store/mine the meme results and it is
compatible with gkdb. I can export the schema for you and the
mining/storing perl modules if you would like.
Sean Davis wrote:
> I am using TFBS::PatternGen::MEME to generate motifs based on a set of
> sequences. I am interested in the e-value and log ratio for each
> motif, but I don't see that in the object. Is there a simple way to
> do find that out? How would others approach the problem of running
> many meme runs (multiple batches of sequences)?
> 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
e-mail: skirov at utk.edu
sao at ornl.gov
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And all these things are swept aside"
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