1 This is Version 2.0.7 of the ViennaRNA Package.
2 ------------------------------------------------
3 See the NEWS and Changelog files for differences to previous versions.
5 The ViennaRNA Package consists of a few stand alone programs and a
6 library that you can link your own programs with.
7 Together with this version we distribute the Kinfold and RNAforester
8 programs. See the README files in the respective sub-directories.
10 The package allows you to
12 - predict minimum free energy secondary structures
13 - calculate the partition function for the ensemble of structures
14 - calculate suboptimal structures in a given energy range
15 - compute local structures in long sequences
16 - predict consensus secondary structures from a multiple sequence alignment
17 - predict melting curves
18 - search for sequences folding into a given structure
19 - compare two secondary structures
20 - predict hybridization structures of two RNA molecules
22 The package includes a Perl5 module that gives access to almost all
23 functions of the C library from Perl.
25 There is also a set of programs for analyzing sequence and distance
26 data using split decomposition, statistical geometry, and cluster methods.
27 They are not maintained any more and not built by default.
29 See the NEWS and Changelog files for changes between versions.
31 Please read the copyright notice in the file COPYING!
33 The package should be easily portable. It is known to compile without
34 modifications at least under
35 SunOS 5.x, IRIX 5.x and 6.x, linux, and windows with the CygWin environment.
36 Other UNIX flavors should present no problems.
37 You need a compiler that understands ANSI C. See the INSTALL file for details.
39 The following executables are provided:
40 RNA2Dfold Compute MFE structure, partition function and representative sample structures of k,l neighborhoods
41 RNAaliduplex Predict conserved RNA-RNA interactions between two alignments
42 RNAalifold Calculate secondary structures for a set of aligned RNA sequences
43 RNAcofold Calculate secondary structures of two RNAs with dimerization
44 RNAdistance Calculate distances between RNA secondary structures
45 RNAduplex Compute the structure upon hybridization of two RNA strands
46 RNAeval Evaluate free energy of RNA sequences with given secondary structure
47 RNAfold Calculate minimum free energy secondary structures and partition function of RNAs
48 RNAheat Calculate the specific heat (melting curve) of an RNA sequence
49 RNAinverse Find RNA sequences with given secondary structure (sequence design)
50 RNALalifold Calculate locally stable secondary structures for a set of aligned RNAs
51 RNALfold Calculate locally stable secondary structures of long RNAs
52 RNApaln RNA alignment based on sequence base pairing propensities
53 RNApdist Calculate distances between thermodynamic RNA secondary structures ensembles
54 RNAparconv Convert energy parameter files from ViennaRNA 1.8 to 2.0 format
55 RNAPKplex Predict RNA secondary structures including pseudoknots
56 RNAplex Find targets of a query RNA
57 RNAplfold Calculate average pair probabilities for locally stable secondary structures
58 RNAplot Draw RNA Secondary Structures in PostScript, SVG, or GML
59 RNAsnoop Find targets of a query H/ACA snoRNA
60 RNAsubopt Calculate suboptimal secondary structures of RNAs
61 RNAup Calculate the thermodynamics of RNA-RNA interactions
62 AnalyseSeqs Analyse sequence data
63 AnalyseDists Analyse distance matrices
65 A couple of useful utilities can be found in the Utils directory.
67 All executables read from stdin and write to stdout and use command line
68 switches rather than menus to be easily usable in pipes.
70 For more detailed information see the man pages. Perl utilities contain
71 POD documentation that can be read by typing e.g.
74 We have included a patched version of D.G. Gilbert's readseq program
75 for those who often process sequence files from databanks. See the
76 the documentation in that directory for details.
78 Since version 2.0 the build-in energy parameters (available as parameter
79 file default.par as well) are taken from:
81 D.H. Mathews et al. (2004),
82 "Incorporating chemical modification constraints into a dynamic programming
83 algorithm for prediction of RNA secondary structure",
84 Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292
88 D.H Turner et al. (2009), "NNDB: The nearest neighbor parameter database
89 for predicting stability of nucleic acid secondary structure",
90 Nucleic Acids Research: 38, pp 280-282
92 For backward compatibility we also provide energy parameters from Turner et al.
93 1999 in the file 'rna_turner1999.par'. Additionally, a set of trained RNA energy
94 parameters from Andronescou et al. 2007 'rna_andronescou2007.par' and two sets
95 of DNA parameters ('dna_mathews1999.par' and 'dna_mathews2004.par') are included
96 in the package as well.
97 The code very rarely uses static arrays, and all programs should work for
98 sequences up to a length of 32700 (if you have huge amounts of memory that
101 If you're a commercial user and find these programs useful, please consider
102 supporting further developments with a donation.
104 The most recent source code and documentation should always be available on
106 http://www.tbi.univie.ac.a/~ivo/RNA
108 We need your feedback! Send your comments, suggestions, and questions to
111 Ivo Hofacker, Spring 2006