[Biopython] MOODS: fast search for position weight matrix matches in DNA sequences.

[Bartek Wilczynski]

Hi,
On Thu, Sep 24, 2009 at 2:27 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Peter and Bartek;
>
> [MOODS paper compared with Biopython]
>> > I was even thinking about
>> > incorporating their code into Biopython, but it's GPL, Instead, I can
>> > make the function using Michiel's code aware of the MOODS package:
>> > i.e. use it if it is installed.
>
> It may be worth contacting the authors with your interest in
> incorporating it. If it improves substantially upon the current C
> code from Michiel and could fit with your interface this makes
> sense. Many times people are not tied to GPL, and they may be
> willing to re-license for inclusion in Biopython.
>
Yes, I'll try to talk to them.


>
> A separate news post mentioning the C option speed and showing usage
> examples from both is a great idea. Responsiveness to new methods is
> the fun part of science.
>
I'll try to write that up and send it to the list.

> This is more a consequence of how scientific publication works. You have
> to get published and to do that you have to prove you are somehow that
> much better than other options, which results in trying to find flaws in
> those options. This would all work smoother if the authors came on the
> Biopython list mentioning the speed issues, you all had this discussion
> then and worked on incorporating their code as it was being developed.
> Then we'd have an integrated implementation today. Doing it after the
> fact is a bit more roundabout, but what can you do.
Exactly.

cheers
Bartek