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

[Peter]

On Tue, Jun 16, 2009 at 12:09 PM, Sweta Dash<swetadash at ymail.com> wrote:
> 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.

As Bartek (author of Bio.Motif) explained, you have to use MEME first
(either on the web, or I think you can download a copy to run locally)
to do a search for a motif. Then you can use Biopython to parse the
MEME output.

There are other tools you might consider instead of MEME, such as
AliceAce, where again Biopython can parse the output (and can also
help you call the AliceAce command line tool).

Peter