[Bioperl-l] free energy of two RNA
cjfields at uiuc.edu
Wed May 19 09:42:56 EDT 2004
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 :
You can get mfold here :
Washington University requires a license for use of the program, but you
can now download it directly.
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:
>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
> > 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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Lab of Dr. Robert Switzer
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