[BioPython] sequence logo with biopython
bartek wilczynski
bartek at rezolwenta.eu.org
Mon Sep 17 09:49:12 UTC 2007
Giovanni Marco Dall'Olio <dalloliogm at gmail.com> wrote:
> Hi,
> is there any way to produce sequence logos[1] with biopython?
>
> I have a set of sequences of the same length, which represent the 5'
> donorsite in a set of introns.
> I wonder if there is a way to to create and display a .png logo
> representation of them, like with this program:
> - http://weblogo.berkeley.edu/
>
Unfortunately, currently there is no solution in biopython to this. You can
however take a look at TAMO, a python library designed for working with
motifs.
http://fraenkel.mit.edu/TAMO/ I'm not sure if you can make png files with it,
but there are ways to at least obtain text version of the logo.
--
regards
Bartek
--
For every complex problem there is an answer that is clear, simple, and wrong.
H. L. Mencken
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