[Bioperl-l] HELP!!! ALIGN TWO SIMPLE DNA SEQ. USING BIOPERL

[Catherine Letondal]

Jason Stajich wrote:
> This has been covered on the list and is in the FAQ I believe.
> pSW is for protein Smith-Waterman alignments only.
> 
> We don't support DNA alignments directly but you can use the EMBOSS
> program 'water' to generate a the best local alignment with smith-waterman
> or 'needle' to generale a Needleman-Wunsch global alignment.  There is an
> interface to EMBOSS programs called Bio::Factory::EMBOSS.  There is an
> example of how to use it in the FAQ.  NB this is only for unix installs.
> 
> -jason

If you do not have Unix nor a local EMBOSS installation, you can use
PiseBioperl. The following script run a needle on a Web server, and feed
the result to the Bio::AlignIO and Bio::SimpleAlign bioperl packages.

http://www-alt.pasteur.fr/~letondal/Pise/PiseBioperl/Examples/needle.pl

You don't need to install Pise for this purpose, just the perl modules
(see http://www-alt.pasteur.fr/~letondal/Pise/#pisebioperl).

> 
> On Tue, 7 May 2002, Ze Cheng wrote:
> 
> > Hello,
> >       Could someone please kindly tell me how to align two DNA sequence
> > using any possible bioperl software. I have tried clustalw in vain with a
> > unresolved segmentation fault (the authors email does not work), pSW which
> > only aligns protein, blast that always give me sth like "Unable to get
> > Karvin-A. score". Besides, bioperl's doc does not tell you how to turn off
> > the filter. I am desperate now. Thank you for any useful information.
> >       ginger
> >
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> >
> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
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--
Catherine Letondal -- Pasteur Institute Computing Center