Vienna RNA Package

RNA Secondary Structure Prediction and Comparison

General information

The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

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 folding).

Documentation

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 secondary structures
• RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
• RNAinverse -- inverse fold (design) sequences with predefined structure
• RNAdistance -- compare secondary structures
• RNApdist -- compare base pair probabilities
• RNAsubopt -- complete suboptimal folding
• RNAplot -- RNA structure drawings in PostScript, SVG, or GML
• RNAcofold -- predict hybrid structure of two sequences
• RNAduplex -- predict possible hybridization sites between two sequences
• RNAalifold -- predict the consensus structure of several aligned sequences
• RNALfold -- predict locally stable structure of long sequences
• RNAplfold -- compute average pair probabilities for local base pairs in long sequences
• RNApaln -- fast structural alignment of RNA sequences using string alignments
• Several small but helpful Perl Utilities

If you want to include our code into your own programs, you should read the documentation for the RNAlib library.
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 details.

Web interfaces for online RNA folding and sequence design

• Structure prediction for moderate size RNAs can be done interactively on our server. Try our RNAfold Web Interface.
• Inverse folding of small RNAs is now also available as a web service. Design your own sequences on our Sequence Design server.
• For accurate prediction of consensus secondary structures from an alignment of related RNA sequences try our brand new alifold server.

To see what we do with our software, take a look at our preprint server. There you'll also find a preprint version of our (Hofacker et.al. 1994) paper describing the first version of the package.
The fold server is described in Nucleic Acids Res. 31: 3429-3431 (2003)

Version 2.0 of the ALIDOT utilities. An add-on for detecting conserved secondary structure motifs.

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 Homepage.
A lot of information on RNA folding can be found on Michael Zuker's RNA page, where you can also download his mfold program.
The RNAstructure program is re-implementation of mfold for windows including a GUI, it is available from the web site of the Turner group
The ESSA program provides several methods for drawing and analyzing RNA secondary structures.
A good starting point for information on RNA structures is the RNA world in Jena.