[Biopython-dev] Support for standalone version of AlignACE motif search program

[Bartek Wilczynski]

Quoting Jeffrey Chang <jefftc at stanford.edu>:

> Hey Bartek,
> 
> Your package looks very nice.  I'd be happy to check it in under 
> Bio.AlignAce.  I am getting ready to put out a release, so it will have 
> to be done after that goes out.
> 
> Please take a look at the documentation for contributing code to 
> Biopython the website at:
> http://www.biopython.org/docs/developer/contrib.html
> 
> In particular, please read the "Submitting Code" section and make sure 
> you agree with it.  Mostly, it is just to make sure that you want to 
> support your code, and that you agree to the Biopython license.  Let me 
> know if everything seems good to you.
> 
> Jeff
> 
I do agree with the license and I'd be happy to support it.

The other thing is that I'll probably be working with other motif Finding tools
as well, and here arises the need of the general class for sequence motifs.
There exists a TFBS module for bioperl (http://forkhead.cgb.ki.se/TFBS/), and it
serves well for my inspiration , but I think that a sequence motif is something
more general than just Transcription Factor Binding Sites. It would be really
great if someone would help me with other possible uses for the sequence motifs. 

looking forward to any comments
   Bartek Wilczyñski