[Bioperl-l] bioperl dna pairwise local alignment

[Heikki Lehvaslaiho]

On Wed, 2002-10-23 at 09:18, Mike Pheasant wrote:
> I have got the Bio::Factory::EMBOSS working, thanks for the tip, but I want
> a solution that doesnt use `backticks` and pass parameters via file io. By
> the way there are deprecated warnings and a prototype ($input) error using
> perl 5.8.0. If I fix that I'll send it in.

I just installed 5.8.0 but these warnings were not visible unless I ran
the individual test. Thanks for pointing this out. They are now fixed.

	-Heikki

> I think I'm going to try linking it into PostgresQL and/or Mysql as
> functions, as I'd like to do joins on high scoring rows. If that works,
> might also try XS into perl as well. If I get the perl one working I'll
> forward it on.
> 
> Anyone know of anyone linking bioinformatic functions directly into the
> databases as SQL functions?
> 
> Cheers,
> 
> Mike.
> 
> > -----Original Message-----
> > From: Ewan Birney [mailto:birney@ebi.ac.uk]
> > Sent: Wednesday, 23 October 2002 5:50 PM
> > To: Elia Stupka
> > Cc: Mike Pheasant; bioperl-l@bioperl.org
> > Subject: Re: [Bioperl-l] bioperl dna pairwise local alignment
> >
> >
> >
> >
> > 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
> > >
> > > ********************************
> > > * http://www.fugu-sg.org/~elia *
> > > * tel:    +65 6874 1467        *
> > > * mobile: +65 9030 7613        *
> > > * fax:    +65 6779 1117        *
> > > ********************************
> > >
> > >
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> > >
> >
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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