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

[Bartek Wilczynski]

On Tue, Jun 16, 2009 at 2:05 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
>> If the conserved motifs can be found out using the MEME module in
>> biopython, kindly tell me how to do so.

> 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).

That is right. In both cases the job is done by the external tool
(usually locally,
after downloading an executable to your computer). In case of AlignACE,
you can run the program from biopython using the following code:

from bio import Motif
command="/opt/bin/AlignACE"
input_file="test.fa"
result=Motif.AlignAce(input_file,cmd=command,gcback=0.6,numcols=10)
motifs=list(Motif.parse(result[1],"AlignAce"))

but you still need a local  AlignAce executable (in this case in
/opt/bin/AlignACE).

hope that helps

Bartek