ViennaRNA Package

A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Amongst other things, our implementations allow you to:

• predict minimum free energy secondary structures
• calculate the partition function for the ensemble of structures
• compute various equilibrium probabilities
• calculate suboptimal structures in a given energy range
• compute local structures in long sequences
• predict consensus secondary structures from a multiple sequence alignment
• predict melting curves
• search for sequences folding into a given structure
• compare two secondary structures
• predict hybridization structures of two RNA molecules

The package includes Perl 5, Python 2, and Python 3 modules that give access to almost all functions of the C library from within the respective scripting languages.

There is also a set of programs for analyzing sequence and distance data using split decomposition, statistical geometry, and cluster methods. They are not maintained any more and not built by default.

The code very rarely uses static arrays, and all programs should work for sequences up to a length of 32,700 (if you have huge amounts of memory that is).

See the NEWS and CHANGELOG.md files for changes between versions.

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Table of Contents

1. Availability
2. Installation
3. Configuration
4. Executable Programs
5. Energy Parameters
6. References
7. License
8. Contact

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Availability

The most recent source code and documentation should always be available through the official ViennaRNA website and through github.

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Installation

For best portability the ViennaRNA package uses the GNU autoconf and automake tools. The instructions below are for installing the ViennaRNA package from source.

See the file INSTALL for a more detailed description of the build and installation process.

Quick Start

Usually you'll simply unpack the distribution tarball, configure and make:

tar -zxvf ViennaRNA-2.4.11.tar.gz
cd ViennaRNA-2.4.11
./configure
make
sudo make install

User-dir Installation

If you do not have root privileges on your computer, you might want to install the ViennaRNA Package to a location where you actually have write access to. Use the --prefix option to set the installation prefix like so:

./configure --prefix=/home/username/ViennaRNA
make install

This will install everything into a new directory ViennaRNA directly into the home directory of user username.

Note, that the actual install destination paths are listed at the end of the ./configure output.

Install from git repository

If you attempt to build and install from our git repository, you need to perform some additional steps before actually running the ./configure script:

1. Unpack the libsvm archive to allow for SVM Z-score regression with the program RNALfold:

cd src
tar -xzf libsvm-3.23.tar.gz
cd ..

2. Install the additional maintainer tools gengetopt, help2man,flex,xxd, and swig if necessary. For instance, in RedHat based distributions, the following packages need to be installed:

   • gengetopt (to generate command line parameter parsers)
   • help2man (to generate the man pages)
   • flex and flex-devel (to generate sources for RNAforester)
   • vim-common (for the xxd program)
   • swig (to generate the scripting language interfaces)

3. Finally, run the autoconf/automake toolchain:

autoreconf -i

After that, you can compile and install the ViennaRNA Package as if obtained from the distribution tarball.

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Configuration

This release includes the RNAforester, Kinfold, Kinwalker, and RNAlocmin programs, which can also be obtained as independent packages. Running ./configure in the ViennaRNA directory will configure these packages as well. However, for detailed information and compile time options, see the README and INSTALL files in the respective subdirectories.

Cluster Analysis

The programs AnalyseSeqs and AnalyseDists offer some cluster analysis tools (split decomposition, statistical geometry, neighbor joining, Ward's method) for sequences and distance data. To also build these programs add --with-cluster to your configure options.

Kinfold

The kinfold program can be used to simulate the folding dynamics of an RNA molecule, and is compiled by default. Use the --without-kinfold option to skip compilation and installation of Kinfold.

RNAforester

The RNAforester program is used for comparing secondary structures using tree alignment. Similar to Kinfold, use the --without-forester option to skip compilation and installation of RNAforester.

Kinwalker

The kinwalker algorithm performs co-transcriptional folding of RNAs, starting at a user specified structure (default: open chain) and ending at the minimum free energy structure. Compilation and installation of this program is deactivated by default. Use the --with-kinwalker option to enable building and installation of Kinwalker.

RNAlocmin

The RNAlocmin program is part of the Basin Hopping Graph Framework and reads secondary structures and searches for local minima by performing a gradient walk from each of those structures. It then outputs an energetically sorted list of local minima with their energies and number of hits to particular minimum, which corresponds to a size of a gradient basin. Additional output consists of barrier trees and Arhenius rates to compute various kinetic aspects. Compilation and installation of this program is activated by default. Use the --without-rnalocmin option to disable building and installation of RNAlocmin.

Scripting Interfaces

The ViennaRNA Package comes with scripting language interfaces for Perl 5, Python 2, and Python 3 (provided by swig), that allow one to use the implemented algorithms directly without the need of calling an executable program. The necessary requirements are determined at configure time and particular languages may be deactivated automatically, if the requirements are not met. You may also switch-off particular languages by passing the --without-perl, --without-python, and/or --without-python3 configure options, e.g.

./configure --without-perl --without-python

will turn-off the Perl 5 and Python 2 interfaces.

Disabling the entire scripting language support alltogether can be accomplished with the --without-swig switch.

Streaming SIMD Extension support

Our latest version contains code that implements a faster multibranch loop decomposition in global MFE predictions, as used e.g. in RNAfold. This implementation makes use of modern processors capability to execute particular instructions on multiple data simultaneously (SIMD - single instruction multiple data, thanks to W. B. Langdon for providing the modified code). Consequently, the time required to assess the minimum of all multibranch loop decompositions is reduced up to about one half compared to the runtime of the original implementation. This feature is enabled by default since version 2.4.11 and a dispatcher ensures that the correct implementation will be selected at runtime. If for any reason you want to disable this feature at compile-time use the following configure flag

./configure --disable-simd

Link Time Optimization (LTO)

To increase the performance of our implementations, the ViennaRNA Package tries to make use of the Link Time Optimization (LTO) feature of modern C-compilers. If you are experiencing any troubles at make-time or run-time, or the configure script for some reason detects that your compiler supports this feature although it doesn't, you can deactivate it using the flag

./configure --disable-lto

OpenMP support

To enable concurrent computation of our implementations and in some cases parallelization of the algorithms we make use of the OpenMP API. This interface is well understood by most modern compilers. However, in some cases it might be necessary to deactivate OpenMP support and therefore transform RNAlib into a C-library that is not entirely thread-safe. To do so, add the following configure option

./configure --disable-openmp

POSIX threads (pthread) support

To enable concurrent computation of multiple input data in RNAfold, RNAcofold, RNAalifold, and for our implementation of the concurrent unordered insert, ordered output flush data structure vrna_ostream_t we make use of POSIX threads. This should be supported on all modern platforms and usually does not pose any problems. In case you want to compile without POSIX threads support for any reason, add the following configure option

./configure --disable-pthreads

SVM Z-score filter in RNALfold

By default, RNALfold that comes with the ViennaRNA Package allows for z-score filtering of its predicted results using a support vector machine (SVM). However, the library we use to implement this feature (libsvm) is statically linked to our own RNAlib. If this introduces any problems for your own third-party programs that link against RNAlib, you can safely switch off the z-scoring implementation using

./configure --without-svm

GNU Scientific Library

The new program RNApvmin computes a pseudo-energy pertubation vector that aims to minimize the discrepancy of predicted, and observed pairing probabilities. For that purpose it implements several methods to solve the optimization problem. Many of them are provided by the GNU Scientific Library, which is why the RNApvmin program, and the RNAlib C-library are required to be linked against libgsl. If this introduces any problems in your own third-party programs that link against RNAlib, you can turn off a larger protion of available minimizers in RNApvmin and linking against libgsl alltogether, using the switch

./configure --without-gsl

Help

For a complete list of all ./configure options and important environment variables, type

./configure --help

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Executable Programs

The ViennaRNA Package includes the following executable programs:

Program	Description
RNA2Dfold	Compute MFE structure, partition function and representative sample structures of k,l neighborhoods
RNAaliduplex	Predict conserved RNA-RNA interactions between two alignments
RNAalifold	Calculate secondary structures for a set of aligned RNA sequences
RNAcofold	Calculate secondary structures of two RNAs with dimerization
RNAdistance	Calculate distances between RNA secondary structures
RNAduplex	Compute the structure upon hybridization of two RNA strands
RNAeval	Evaluate free energy of RNA sequences with given secondary structure
RNAfold	Calculate minimum free energy secondary structures and partition function of RNAs
RNAheat	Calculate the specific heat (melting curve) of an RNA sequence
RNAinverse	Find RNA sequences with given secondary structure (sequence design)
RNALalifold	Calculate locally stable secondary structures for a set of aligned RNAs
RNALfold	Calculate locally stable secondary structures of long RNAs
RNApaln	RNA alignment based on sequence base pairing propensities
RNApdist	Calculate distances between thermodynamic RNA secondary structures ensembles
RNAparconv	Convert energy parameter files from ViennaRNA 1.8 to 2.0 format
RNAPKplex	Predict RNA secondary structures including pseudoknots
RNAplex	Find targets of a query RNA
RNAplfold	Calculate average pair probabilities for locally stable secondary structures
RNAplot	Draw RNA Secondary Structures in PostScript, SVG, or GML
RNApvmin	Calculate a perturbation vector that minimizes discripancies between predicted and observed pairing probabilities
RNAsnoop	Find targets of a query H/ACA snoRNA
RNAsubopt	Calculate suboptimal secondary structures of RNAs
RNAup	Calculate the thermodynamics of RNA-RNA interactions
AnalyseSeqs	Analyse sequence data
AnalyseDists	Analyse distance matrices

A couple of useful utilities can be found in the src/Utils directory.

All executables read from stdin and write to stdout and use command line switches rather than menus to be easily usable in pipes. For more detailed information see the man pages. Perl utilities contain POD documentation that can be read by typing e.g.

perldoc relplot.pl

Together with this version we also distribute the programs

• kinfold,
• RNAforester,
• RNAlocmin, and
• kinwalker

See the README files in the respective sub-directories.

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References

If you use our software package, you may want to cite the follwing publications:

• R. Lorenz et al. (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology, 6:26

• I.L. Hofacker (1994), "Fast folding and comparison of RNA secondary structures", Monatshefte fuer Chemie, Volume 125, Issue 2, pp 167-188

Note, that the individual executable programs state their own list of references in the corresponding man-pages.

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Energy Parameters

Since version 2.0.0 the build-in energy parameters, also available as parameter file rna_turner2004.par, are taken from:

• D.H. Mathews et al. (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292

• D.H. Turner et al. (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282.

For backward compatibility we also provide energy parameters from Turner et al. 1999 in the file rna_turner1999.par.

Additionally, a set of trained RNA energy parameters from Andronescou et al. 2007, rna_andronescou2007.par, a set of RNA energy parameters obtained by graft and grow genetic programming from Langdon et al. 2018, rna_langdon2018.par, and two sets of DNA parameters, dna_mathews1999.par and dna_mathews2004.par, are included in the package as well.

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License

Please read the copyright notice in the file COPYING!

If you're a commercial user and find these programs useful, please consider supporting further developments with a donation.

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Contact

We need your feedback! Send your comments, suggestions, and questions to [email protected]

Ivo Hofacker, Spring 2006