[BioPython] [Biopython-dev] Refactoring motif analysis code

[Bruce Southey]

Bartek Wilczynski 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).
>   
Actually I am not that thrilled with the licenses for these packages and 
similar packages because these are free only for academic use. To me 
this clashes with the spirit of an open-sourced project especially a 
BSD-licensed one. But if there is a need for such modules then these 
modules should be included.

> 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
>
>   
While it is only free for academic use, have you seen TAMO?
*TAMO: a flexible, object-oriented framework for analyzing 
transcriptional regulation using DNA-sequence motifs. *
Bioinformatics. 2005 Jul 15;21(14):3164-5. 
<http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/14/3164>

http://fraenkel.mit.edu/TAMO/


> 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?
>   
Well, I am not sure how many used Bio.AlignAce given the Parser.py bug :-)
Based on the CVS, both have been untouched for about three years.

Also, what species are these used for?
One of the papers of AlignAce indicate that the base composition was set 
for yeast.

> - 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
>
>   
Personally I would be interested in a general protein motif finding 
module because of my current research. However, I do have a different 
view with respect to the Biopython community as indicated above with the 
licenses.

Bruce