[Bioperl-l] comparing two seq

[Heikki Lehvaslaiho]

Vesko,

Perl is really not language to write CPU intensive applications, so the
only sequence comparison implementations we have in bioperl are written
in C and are not part of the standard distribution. Look for bioperl-ext
cvs module.

What we try to do is to have perl wrappers for other programs. Check
e.g.the EMBOSS suite at http://www.emboss.org/. The best program we have
a wrapper for for rna/dna alignments is Sim4. The wrappers are all in
the separate run module in cvs or tar file:
http://www.bioperl.org/DIST/current_run_stable.tar.gz

Sim4 can be tricky to compile so check if there is a binary for your
platform. For example,  I've seen an RPM file for Mandrake Linux.

	-Heikki


On Thu, 2003-09-04 at 12:19, Vesko Baev wrote:
> Hi,
> Which way is the best (and which module is best to use)for comparing two sequnces (rna & dna)?
> 
> thanks a lot friends!
> 
> Vesko
> Plovdiv,BULAGRIA
> 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
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