RNA secondary structure software

micha at amber.biophys.uni-duesseldorf.de micha at amber.biophys.uni-duesseldorf.de
Fri Jan 13 15:57:16 EST 1995

Neil Brockdorff x3247 (nbrockdo at hgmp.mrc.ac.uk) wrote:
: I am looking for the best available RNA secondary structure programs. 
: I have used GCG and pc software but find it somewhat restricted and 
: unfriendly.  Any suggestions?

My suggestion: use GCG's MFOLD (hope the X-environment makes it
easier to use) or get the RNAFold package from :
ftp.itc.univie.ac.at (Vienna, Austria).

MFold is based on the Zuker-Nussinov method and predicts optimal as well
as suboptimal foldings, whereas RNAfold is based on McCaskill's partiton
function algorithm - this permits predicting the basepair probability
distribution directly. (Caution: no individual suboptimal structures 
produced by this program; only optimal folding is presented as calculated by
Zuker's method)

Both programs let you run structure prediction at various temperatures, MFOLD
has an option to exclude 'unwanted' base pairings.

A user-friendly front end missing? As far as I know, there is none available
for RNAfold, but it could be done by Perl or Tk/Tcl on Unix.

And could you explain the restrictions you complain about somewhat more
detailed ??


	Michael Schmitz
	Biophysics Dept., U. Duesseldorf

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