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README
This is Version 2.0.7 of the ViennaRNA Package.
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See the NEWS and Changelog files for differences to previous versions.
The ViennaRNA Package consists of a few stand alone programs and a
library that you can link your own programs with.
Together with this version we distribute the Kinfold and RNAforester
programs. See the README files in the respective sub-directories.
The package allows you to
- predict minimum free energy secondary structures
- calculate the partition function for the ensemble of structures
- 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 a Perl5 module that gives access to almost all
functions of the C library from Perl.
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.
See the NEWS and Changelog files for changes between versions.
Please read the copyright notice in the file COPYING!
The package should be easily portable. It is known to compile without
modifications at least under
SunOS 5.x, IRIX 5.x and 6.x, linux, and windows with the CygWin environment.
Other UNIX flavors should present no problems.
You need a compiler that understands ANSI C. See the INSTALL file for details.
The following executables are provided:
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
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 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
We have included a patched version of D.G. Gilbert's readseq program
for those who often process sequence files from databanks. See the
the documentation in that directory for details.
Since version 2.0 the build-in energy parameters (available as parameter
file default.par as well) 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
and
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' and two sets
of DNA parameters ('dna_mathews1999.par' and 'dna_mathews2004.par') are included
in the package as well.
The code very rarely uses static arrays, and all programs should work for
sequences up to a length of 32700 (if you have huge amounts of memory that
is).
If you're a commercial user and find these programs useful, please consider
supporting further developments with a donation.
The most recent source code and documentation should always be available on
the web at
http://www.tbi.univie.ac.a/~ivo/RNA
We need your feedback! Send your comments, suggestions, and questions to
rna@tbi.univie.ac.at
Ivo Hofacker, Spring 2006
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