This is Version 1.8.x of the Vienna RNA Package. ------------------------------------------------ See the NEWS and Changelog files for differences to previous versions. The Vienna RNA packages 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: RNAfold predict secondary structures RNAsubopt calculate suboptimal structures in a given energy range RNAalifold predict a consensus structure for a set of aligned sequences RNAcofold calculate the hybrid structure of two RNA molecules RNAduplex predict possible hybridization sites for two RNAs RNAeval evaluate energy for given sequence and structure RNALfold calculate locally stable RNA secondary structures RNAheat calculate melting curves RNAdistance compare secondary structures RNApdist compare ensembles of secondary structures RNAinverse find sequences folding into given structures RNALfold predict locally stable structure of long sequences RNAplfold compute average pair probabilities for local base pairs in long sequences 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. Versions since 1.4 feature energy parameters as described in Mathews et.al, JMB, 1999. For backward compatibility a parameter file with the version 1.3 parameter set (as described in Walter et.al (1994)) can be found in the file vienna13.par. The standard energy set is compiled in, but can also be found in the file default.par. Note that only free energies at 37C are new. Temperature dependencies are still derived from the old parameter set. 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.at/~ivo/RNA/ We need your feedback! Send your comments, suggestions, and questions to rna@tbi.univie.ac.at Ivo Hofacker, Spring 2006