[Bioperl-l] writing a pairwise alignment module: XS and Inline C?

[Adam Kraut]

The program generates an ensemble of weighted suboptimal alignments by use
of a partition function and stochastic backtracking.  The algorithm is quite
novel and it's really only part of a larger multi-scale comparative modeling
project. There documentation is here:

http://www.tbi.univie.ac.at/~ulim/probA/probA_lib.html

While I think this would be useful to the bioperl community if it were fully
abstracted/extended, I would at the least like to be able to pass in any two
sequences and get back SimpleAlign objects for our internal uses first.  I
have a good idea on how to get started.  I will be sure to post when I get
into trouble.


On 5/19/06, aaron.j.mackey at gsk.com <aaron.j.mackey at gsk.com> wrote:
>
> bioperl-ext is the package in which alignment algorithms and/or BioPerl
> "wrapped" external C libraries live.  Subprojects in bioperl-ext use both
> XS and Inline::C, that's up to you.
>
> You'll need to get your C code compiled to a dynamically loaded library
> (.so) to use either XS or Inline::C; this precludes any reuse of the C
> main() function (although your Inline::C wrapper might recapitulate/copy
> the main() function code).
>
> Out of curiosity, what pairwise alignment algorithm are you using?  This
> is a heavily beaten path, you might want to dig around first to see if
> someone else already has what you need.
>
> -Aaron
>
>