[Bioperl-l] comparing two seq

[Marc Logghe]

> -----Original Message-----
> From: Heikki Lehvaslaiho [mailto:heikki at ebi.ac.uk]
> Sent: Thursday, September 04, 2003 4:49 PM
> To: Vesko Baev
> Cc: Bioperl
> Subject: Re: [Bioperl-l] comparing two seq
> 
> 
> 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.

Also for RH and Suse on http://www.biolinux.org/sim4.html
ML