[Bioperl-l] GCG and Perl

[Freimuth,Robert]

> Date: Tue, 06 Jan 2004 17:30:04 +0100
> From: Laurence Amilhat <Laurence.Amilhat at clermont.inra.fr>
> Subject: [Bioperl-l] GCG and Perl
> 
> I would like to run GCG programs in a Perl script (such as 
> bestfit), but I cannot make it work.
> I know that there are BioPerl modules to run EMBOSS program, 
> but I don't have Emboos installed in my system.
> Does anyone have an idea?

>> Date: Tue, 6 Jan 2004 11:53:11 -0500
>> From: "Brian Osborne" <brian_osborne at cognia.com>
>> Subject: RE: [Bioperl-l] GCG and Perl
>> 
>> If there's a program in the EMBOSS suite that can functionally replace
>> bestfit then you could install EMBOSS and use it. Is there 
>> any reason you
>> can't do this? What kind of computer are you using?
>> 
>> Brian O.

Hi Laurence,

A few years ago (during my pre-perl years) I wrote some unix shell scripts to
call bestfit and/or gap, so I know it's possible to call GCG programs from
the command line.  What have you tried?

That said, I agree with Brian: EMBOSS has a lot of great tools, so you may
want to look into installing it (the two alignment programs you'd probably be
most interested in are 'needle' and 'water').  The one catch is that it
requires a *nix OS, so if you're running Windows you'll need to look into
Cygwin.

Finally, take a look at the pSW module in Bio::Tools, if you want to call a
local alignment algorithm from perl.  There isn't a global alignment module
yet, AFAIK, but if you need one you could try to tweek pSW.  Alternatively, I
wrote a needleman-wunsch module that I would be happy to share, but it's far
from optimized and (since I'm still quite the beginner) probably fairly ugly
code.

Bob


Robert Freimuth, PhD
Post-Doctoral Fellow
Washington University School of Medicine
Department of Internal Medicine
Division of Molecular Oncology