[Bioperl-l] RNA analysis

Chris Fields cjfields at uiuc.edu
Mon Mar 15 11:24:03 EST 2004

I agree with Jason.  Although MFOLD seems to be the most commonly used 
program, the Vienna package is the only program I know of that releases its 
code w/o strict licensing requirements.  And it comes with Perl interfaces 
to its programs, although these aren't related to Bioperl.  A potentiual 
problem is that modules may not compile under Perl 5.8, according to the 
web page (I personally haven't tried this out).

There are also interfaces to the Institute Pasteur's online Pise 
applications (versions of MFOLD and the Vienna package included) in 
Bioperl-Run.  Again, I haven't tried these out, although I plan on looking 
through them to see if they can also be used for locally installed programs.

I'm hoping to have something up in the next months on a couple of programs 
(RNAmotif and ERPIN), but an MFOLD module will probably take a little 
longer due to other commitments (i.e. my job, see below).  I think your 
best bet at the moment is using the Vienna package Perl modules.


At 09:18 AM 3/13/2004, Jason Stajich wrote:
>See ViennaRNA package from Ivo Hofacker's group and their RNAFold.pl
>script - there is a nice XS perl interface to the C library.
>On Sat, 13 Mar 2004, Vesko Baev wrote:
> > Is there a bioperl module(s) for RNA analysis: folding, free energy,
> > RNA/RNA align or modules that connect the script with ext. RNA progs?
> >
> > Thenks!
> > Vesko
> >
> > -----------------------------------------------------------------
> > http://zavedenia.gbg.bg - Êúäå ùå õîäèòå òàçè âå÷åð?
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org


Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer


University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
600 S. Mathews Ave.
Urbana, IL 61801

Phone : (217) 333-7098
Fax : (217) 244-5858 

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