[Biopython-dev] Refactoring motif analysis code

[Giovanni Marco Dall'Olio]

On Mon, Nov 24, 2008 at 3:51 PM, Bartek Wilczynski
<bartek at rezolwenta.eu.org> wrote:
> Hello All,
>
> Currently, there are two packages dealing with motif analysis in biopython :
> Bio.AlignAce (written by me) and Bio.MEME (written by Jason Hackney).

Hi, I asked a question about motifs one year ago on this list.
Here it is the thread:
- http://lists.open-bio.org/pipermail/biopython/2007-September/003727.html

I would just like to tell you that I have tried the TAMO framework you
suggested me, and found it very useful.
I am not using it anymore because I don't need it, but I remember that I liked:
- the methods to represent motifs as matrixes of frequencies/occurrencies etc..
- the fact that it was easy to create a motif from an alignment of sequences
- the integration it had with this website:
http://weblogo.berkeley.edu/logo.cgi.
I would suggest you to provide integration with this other web
service, which enable to plot the difference between two sequence
logos: http://www.twosamplelogo.org/examples.html.

Maybe you should contact TAMO's author to ask him if he wants to
contribute, because I remember that its framework was really complete.


>
> Both of them are quite old and they were developed independently so
> the functionality is largely overlapping.
> Particularly the files AlignAce/Motif.py  and MEME/Motif.py contain
> almost identical functionality useful for
> anyone interested in motif analysis of  writing a parser for yet
> another motif searching tool.
>
> I'd like to change this and create a new library called Bio.Motif,
> which would contain:
> -Motif class for all general functionality concerning motif objects:
> i/o, comparisons, sequence scanning
> -AlignAce Parser
> -MEME Parser
>
> When this is completed, we could deprecate the AlignAce and MEME
> modules. For AlignAce I have most of the code
> already written, I need to rewrite portions of MEME parser to work
> with different motif implementation (not a major pain).
> Then I just need to polish it a bit and provide tests and a short tutorial.
>
> After this rather long intro I'd like to ask about several things:
> - Are there many Bio.AlignAce or Bio.MEME users who would be unhappy
> about deprecating them?
> - Are there any features which people would find valuable in Bio.Motif
> - Both MEME and AlignAce are DNA-oriented, I've never worked on
> Protein motifs myself, but I'd like to know whether anyone is
> interested in using Bio.Motif for that
>
> Any comments/ideas are welcome
>
> cheers
> Bartek
>
> --
> Bartek Wilczynski
> ==================
> Postdoctoral fellow
> EMBL, Furlong group
> Meyerhoffstrasse 1,
> 69012 Heidelberg,
> Germany
> tel: +49 6221 387 8433
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