[Bioperl-l] free energy of two RNA

[Chris Fields]

I'll repost my response b/c I didn't see it pop up on the newsgroup.

Does the Vienna package calculate the free energy of binding between two 
RNA molecules (i.e. hybridization)?  I think it only calculates the free 
energy of folding from a single RNA but I could be wrong (I've never used 
it for that).

Michael Zuker has an online resource to calculate free energy of 
hybridization and melting temp (Tm) between DNA and RNA molecules.  I think 
it may be part of the mfold package.  There isn't a Bioperl module for 
running the program or parsing the output, though.

The online version is :

http://www.bioinfo.rpi.edu/applications/mfold/old/rna/form6.cgi

You can get mfold here :

http://www.bioinfo.rpi.edu/~zukerm/rna/mfold-3.1.html

Washington University requires a license for use of the program, but you 
can now download it directly.

Chris

At 08:20 AM 5/18/2004, Adam Woolfe wrote:
>There's unlikely to be a Bioperl module but there is an external web site
>which is likely to have something for you:
>
>http://www.tbi.univie.ac.at/~ivo/RNA
>
>Adam
>
>Adam Woolfe
>Comparative Genomics Group
>MRC Rosalind Franklin Centre for Genomics Research
>Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
>Tel: +44 1223 494501  Fax: +44 1223 494512
>E-mail: awoolfe at rfcgr.mrc.ac.uk  Web: http://www.rfcgr.mrc.ac.uk
>
>On Tue, 18 May 2004 baev at imbb.forth.gr wrote:
>
> > Hello,
> > I have to calculate the free energy of binding of two RNA molecules. Is 
> there
> > a module in BioPerl that I can use or module to external program?
> >
> > Thanks in advance!
> > Sincerely Yours Vesselin Baev.
> >
> >
> > -----------------
> > University of Plovidv
> > Biology Faculty
> > Cell Biology Lab
> > baev at pu.acad.bg
> >
> >
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> >
>
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__________________________________

Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer

Address:

University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
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Phone : (217) 333-7098
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