Vienna RNA Package

RNA Secondary Structure Prediction and Comparison

News in short

Current version of the Vienna RNA Package is 1.8.4, download the source distribution here.
Some recently added features:
The RNAup program for computing RNA-RNA interactions is now included.
Folding of circular RNAs is now supported in many of the programs
support for computing hybrid structures using RNAcofold, RNAup, RNAduplex, and RNAaliduplex.
stochastic backtracking to produce Boltzmann weighted ensembles of suboptimal structures (try RNAsubopt -p 10).
Local versions of the folding algorithms for scanning large sequences (genomes): RNALfold and RNAplfold
RNAplfold can now be used to compute local accessibilities
Several new utilities e.g. for color annotated structure plots, consensus structures and alignments.
The Vienna RNA package now distributes two related but separate pieces of software:
- The RNAforester, written by Matthias Hoechsmann <mhoechsm@techfak.uni-bielefeld.de>, computes tree-alignments of RNA structures
- The kinfold program explores the folding kinetics of RNA molecules through simulation of stochastic folding trajectories.
Windows users see our page about running the Vienna RNA package under Windows, including a several precompiled binaries.

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

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.

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.

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 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.

Ivo Hofacker, <ivo@tbi.univie.ac.at>
Institut für theoretische Chemie, Währingerstr. 17,
A-1090 Wien, Austria

Member of the RNA webring
[ << Prev | Ring Hub | Random | Next >> ]

Last modified: 2007-12-18 11:54:24 ivo