[Biopython] Seeking assistance to use Bio.MEME in biopython

[Bartek Wilczynski]

On Tue, Jun 16, 2009 at 11:13 AM, Peter<biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Jun 16, 2009 at 9:53 AM, Sweta Dash<swetadash at ymail.com> wrote:
>> Hello Group,
>>           I have many probe sequences for which I want to find
>> the conserved motifs using the Bio.MEME module in python.
>> There  are not many solutions on the net. So, Kindly tell me
>> how to use the module in python for which I shall be very grateful.
>
> Are you already familiar with the MEME tool? That would certainly
> be important here... see http://meme.sdsc.edu/
>
> It might help if you went into a little more detail. Are you working
> with nucleotides or proteins? Have you already identified a motif
> "by eye" for which you want to construct a model?
>
> Also note that Bio.MEME and Bio.AligneAce are being phased
> out in favour of Bio.Motif, so if you are writing new code you
> should start with Bio.Motif rather than Bio.MEME. You'll need
> Biopython 1.50 for this. Try this for some basic help:
>
>>>> from Bio import Motif
>>>> help(Motif)
>
> Or read the docstrings online here:
> http://biopython.org/DIST/docs/api/Bio.Motif-module.html
>

Hi,

If you want to use Bio.Motif to parse your output from MEME, you can just write

from Bio import Motif
motifs = list(Motif.parse(open("meme.out"),"MEME"))

to get the output of MEME (from file "meme.out") to a list of motifs.

As Peter pointed out, the actual search is done by the MEME software,
so you need to run it yourself first on your sequences.

cheers
-- 
Bartek Wilczynski
==================
Postdoctoral fellow
EMBL, Furlong group
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69012 Heidelberg,
Germany
tel: +49 6221 387 8433