The Vienna RNA Package consists of a C code library and several
stand-alone programs for the prediction and comparison of RNA
RNA secondary structure prediction through energy minimization
is the most used function in the package. We provide three kinds of
dynamic programming algorithms for structure prediction: the
minimum free energy algorithm of (Zuker & Stiegler 1981) which
yields a single optimal structure, the partition function algorithm
of (McCaskill 1990) which calculates base pair probabilities in the
thermodynamic ensemble, and the suboptimal folding algorithm of
(Wuchty et.al 1999) which generates all suboptimal structures
within a given energy range of the optimal energy. For secondary
structure comparison, the package contains several measures of
distance (dissimilarities) using either string alignment or
tree-editing (Shapiro & Zhang 1990). Finally, we provide an
algorithm to design sequences with a predefined structure (inverse
For a detailed information, take a look at the HTML versions of the man
pages for the programs and the manual of the library below.
RNAfold -- predict minimum energy
secondary structures and pair probabilities
RNAeval -- evaluate energy of RNA
RNAheat -- calculate the specific
heat (melting curve) of an RNA sequence
RNAinverse -- inverse fold
(design) sequences with predefined structure
If you want to include our code into your own programs, you should
read the documentation for the RNAlib
When installing from source, see the installation instructions.
The package is free software and can be downloaded as C source
code that should be easy to compile on almost any flavor of Unix
and Linux. See the README file for
Web interfaces for online RNA folding and sequence design
For those who don't want to install programs or need a ghraphical
interface, most of the above programs are now accessible from our brand new
Vienna RNA WebServers.
Services include single sequence folding, alignment folding, inverse
folding RNA-RNA interactions, structural alignment, ncRNA detection, and
more. Note that all servers will give hints how to accomplish the same
thing using the command line tools.
Version 2.0 of the ALIDOT utilities. An
add-on for detecting conserved secondary structure motifs.
Old versions of the Vienna RNA package can be downloaded from our history page.
RNA folding software from elsewhere
Ole Matzura's has written a program for 32-bit Windows based on the
RNA folding routines in the Vienna package with a nice graphical
user interface, see the Rnadraw
A lot of information on RNA folding can be found on Michael Zuker's RNA
page, where you can also download his mfold
The RNAstructure program is re-implementation of
mfold for windows including a GUI, it is available
from the web site of the Turner group
program provides several methods for drawing and analyzing RNA
A good starting point for information on RNA structures is the
RNA world in Jena.
Institut für theoretische Chemie, Währingerstr. 17,
A-1090 Wien, Austria