[Bioperl-l] RNA folding

[Sourav Bandyopadhyay]

    I havent heard/seen anything on this feature in the bioperl project. 
I have run across some open source applications that may be of help in 
analyse pre-folded sequences. You should take a look at ViennaRNA 1-4 by 
Ivo Hofacker.
 http://www.tbi.univie.ac.at/~ivo/RNA/
This also includes some C libraries that can help you evaluate RNA 
stuctures given the sequence and the structure in bracket notation. 
Specifically RNA::energy_of_struct . These libraries account for Zuker 
thermodynamics. Take a look, I hope that helps.

-Sourav

David J. Evans wrote:

>Bioperlers,
>Anyone out there using bioperl to analyse RNA secondary
>structures ?  I've dabbled with some of the modules for some
>amateur covariance analysis, but now need to implement the
>thermodynamic calculations on known structures.  This is not
>large scale number crunching, which I'd do using MFOLD or
>similar.  Rather, I want to rapidly analyse hundreds of
>short pre-folded sequences.
>If anyone has the thermodynamic data implemented as a module
>I'd be interested in hearing from you.
>Regards
>David
>
>
>==============
>David J. Evans
>Institute of Virology :: david.evans@vir.gla.ac.uk
>University of Glasgow :: Tel/Fax +44 141 330 6249
>Church Street         :: Mobile  +44 7940 592768
>GLASGOW  G11 5JR  UK  :: www.polio.vir.gla.ac.uk
>
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-- 
Sourav Bandyopadhyay

Informatics Programmer
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