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DNA folding

Peter Stadler stadler at SantaFe.edu
Wed Jun 29 19:31:34 EST 1994


Alex Borovkov (borovkov at plains.NoDak.edu) wrote:
: does anybody know any software for DNA folding. For RNA folding I've been 
: using PCfold and RNAfold, but these softwares don't have a DNA folding 
: option. In order to use them for folding DNA the energy file need to be 
: modified, but I don't know how.

Hi! 

We would be glad to incorporate a DNA folding option into the 
"Vienna RNA Package" [available by anonymous ftp from
ftp.itc.univie.ac.at ] if somebody out there in the net could 
provide as with energy parameters suitable for DNA. We had the
request for DNA folding before, but the few thermodynamic data 
measured for DNA that we stumbled across so far were not sufficient
to provide a complete set of parameters. We would be grateful for
any hint regarding such data. 

Yours,    

Peter F Stadler, Theoretical Biochemistry, Institute for Theoretical
Chemistry, Univ of Vienna, Austria, & Santa Fe Institute, Santa Fe, NM.





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