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
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
Biophysics Dept., U. Duesseldorf