[Bioperl-l] RNA fold

[Chris Fields]

I think, like the rest, that RNAFold may be the easiest way to go.  
mfold is a free program but distribution is bound up by licensing 
issues (I have it but can't redistribute it due to this; the web 
interfaces available have some limitations which I couldn't do 
without).  RNAFold doesn't have these problems and the source code is 
available on the web, plus (like Jason pointed out) there are perl 
interfaces.  There is also something in the book Genomic Perl on 
calculating energies and drawing secondary structures, but I haven't 
checked it out in detail.

Personally, I am working on a bioperl parser for the RNAmotif program 
suite (used to search for conserved secondary structures based on a 
descriptor).  The rnamotif program is able to pass the motif hits to 
efn or efn2 for calculating free energy (based on different energy 
rules) and can output CT format files.  I'm also thinking about doing 
something similar for tRNAscan-SE and ERPIN at some point.  The problem 
I'm running into is how to store the secondary structure output for 
inclusion into GFF databases (I'm currently using 
Bio::SeqFeature::Generic for storing features).  Anyone?

Chris Fields
Postdoctoral Reseacher - Dept. of Biochemistry
University of Illinois at Urbana-Champaign

On Dec 5, 2003, at 2:22 PM, Vesko Baev wrote:

> Hi to all,
> if anyone knows a module or external program (which can be linked to 
> bioperl) for folding a RNA predicting hairpins and calculating a free 
> energy?
>
> Thanks to ALL!
>
> Vesselin Baev
> Bulgaria
>
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