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ViennaRNA At ABCC
Name: 
ViennaRNA
Version(s): 
1.4
Category: 
Molecular Modeling; RNA Analysis, Sequence Analysis, Bioinformatics
Author(s)/Vendor(s): 
Ivo Hofacker (ivo@tbi.univie.ac.at) with contributions from
Peter Stadler, Walter Fontana, and Stefan Wuchty
Program Description: 
The Vienna RNA packages consists of a few stand alone programs and a
library that you can link your own programs with. The package allows
you to

- predict minimum free energy secondary structures
- calculate the partition function for the ensemble of structures
- calculate suboptimal structures in given energy range
- predict melting curves
- search for sequences folding into a given structure
- compare secondary structures including pairwise alignment.

There is also a set of programs for analysing sequence and distance
data using split decomposition, statistical geometry, and cluster
methods.

The following executables are provided:
RNAfold         predict secondary structures
RNAsubopt       calulate suboptimal structures in a given energy
range
RNAeval         evaluate energy for given sequence and structure
RNAheat         calculate melting curves
RNAdistance     compare secondary structures
RNApdist        compare ensembles of secondary structures
RNAinverse      find sequences folding into given structures
AnalyseSeqs     analyse sequence data
AnalyseDists    analyse distance matrices
RNAplot
Computer platform(s): 
SGI, Linux
Location: 
/usr/local/fbscapp/ViennaRNA-1.4
Access: 
Account on ABCC's SGI or Linux systems is required.

To use ViennaRNA programs and scripts you need to add to your
path their location:
 set path = ($path /usr/local/fbscapp/ViennaRNA-1.4)
Documentation: 
Man pages are available at
/usr/local/fbscapp/ViennaRNA-1.4/man for the following
programs: AnalyseDists, RNAeval, RNAinverse, RNAsubopt,
AnalyseSeqs, RNAfold, RNApdist, RNAdistance, RNAheat, and
RNAplot. 

To use the man pages:
 man -M /usr/local/fbscapp/ViennaRNA-1.4/man RNAplot
or modiy you MANPTH environment by including
/usr/local/fbscapp/ViennaRNA-1.4/man in it.

The RNAlib library is documented in the files RNAlib.pdf,
RNAlib.info, and RNAlib.html located in the
/usr/local/fbscapp/ViennaRNA-1.4/man directory.
Web Site: 
http://www.tbi.univie.ac.at/~ivo/RNA/
ABCC Contact Person: 
Sarnagan Ravichandran
301-8461991
sravi@ncifcrf.gov
Created By: 
miaskiew
Created Time: 
2002-06-03
Updated By: 
miaskiew
Updated Time: 
2002-06-03
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