RNA secondary structure analysis

Ivo Hofacker ivo at tbi.univie.ac.at
Fri Oct 31 08:04:23 EST 1997

sofie van Huffel (sofie at lmb1.rug.ac.be) wrote:
: Hi,
: Could anyone point me to a website or a program where I could analyse
: secondary structures of RNA?
: I want to analyze RNA sequences of about 500-600 bp long.
: Thanks for your help,

: Sofie at lmb1.rug.ac.be

If you only have a few sequences Michael Zukers mfold server is the
option. You'll find his home page at http://www.ibc.wustl.edu/~zuker/.
There's another prediction server by V. Skulachev at 
http://www.genebee.msu.su/services/rna2_full.htm, but I know very little
about their method. 
For a larger number of sequences you might want to install an RNA
folding program on your own machine. The following programs all predict
RNA structures from thermodynamic parameters:

- the Vienna RNA package, available from my home page at
  http://www.univie.ac.at/~ivo/RNA/ (C source code)
- Ole Matzura's RNAdraw for windows from http://rnadraw.base8.se/, which
  uses the Vienna algorithms, but adds a nice GUI.
- Zukers mfold-2.3 is available from his home page (fortran source
code    and some binaries)
- David Mathews RNAstructure for Win95 is based on mfold and
available     at http://rna.chem.rochester.edu/RNAstructure.html 


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