[Bioperl-l] bioperl dna pairwise local alignment

[Ewan Birney]

On Wed, 23 Oct 2002, Elia Stupka wrote:

> > Has anyone linked the water.c code from EMBOSS into perl ?
> > Are there any other perl modules anyone knows about which do this?
>
> No, but you can run EMBOSS within bioperl, see the synopsys of the EMBOSS
> module, Bio::Factory::EMBOSS, which has an example using water...

Unless you are doing something pretty impressive (like aligning 50mers)
then the systems overhead should be small vs the alignment code.


BTW - you can force pSW to do the alignments by "pretending" that the
dna sequences are protein and making a "protein" matrix which looks like
DNA, but I suspect that you will want things like gap-end penalty and
semi-local alignments.


If you feel up to it - take a look at Wise2 package and the program dnal -
you then need to build XS bindings into that function - get an idea from
things like gwrap.xs in the wise2/src/models directory. not for the faint
hearted of course.




>
> Elia
>
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