[Bioperl-l] MEME parsing

Stefan Kirov skirov at utk.edu
Tue Nov 9 15:33:13 EST 2004

Hi Sean,
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)?
> Thanks,
> Sean
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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"

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