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

[Sweta Dash]

Hi Peter,
              Thanks for your kind reply. My goal is to find out conserved motifs in nucleotide sequences. Can I do this using the MEME module in biopython or do I have to use the web MEME tool and parse the output through biopython. 

If the conserved motifs can be found out using the MEME module in biopython, kindly tell me how to do so.

With regards,
Sweta Dash

--- On Tue, 6/16/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

From: Peter <biopython at maubp.freeserve.co.uk>
Subject: Re: [Biopython] Seeking assistance to use Bio.MEME in biopython
To: "Sweta Dash" <swetadash at ymail.com>
Cc: biopython at biopython.org
Date: Tuesday, June 16, 2009, 9:13 AM

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

Peter