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ANNOUNCE: Package for Folding and Comparing RNA Secondary Structures

Ivo Hofacker ivo at tiger
Thu Apr 29 16:08:43 EST 1993


The Vienna RNA Package, a new package for folding and comparing RNA
secondary structures is now available by anonymous ftp from
ftp.itc.univie.ac.at. 

It 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 and base pairing probabilities for
  the ensemble of structures.
- predict melting curves.
- search for sequences folding into a given structure (inverse folding).
- compare secondary structures including pairwise alignment.

The folding routines are based on a variant of the dynamic folding
algorithm by Zuker and Stiegler, and a similar algorithm for
calculating the partition function for the ensemble of possible
secondary structures by John McCaskill. Structures can be compared
using string- and tree-editing.

There is also a set of programs for analysing sequence and distance
data using split decomposition, statistical geometry, and cluster methods.
This part of the package has not yet been tested extensively.

The package is known to compile on
SUN Sparcs, IBM RS600, HP 720, and Silicon Graphics workstations.
Porting to other UN*X machines should present no problems.
You need a compiler that understands ANSI C.

To get the package do:

prompt> ftp ftp.itc.univie.ac.at
Name (ftp:you): anonymous
Password: your_email_adress
ftp> cd pub/RNA
ftp> bin
ftp> get ViennaRNA-1.0.tar.Z
ftp> bye


--
+--------------------------------------+-------------------------------------+
| Ivo Hofacker                         |       	       	 		     |
|				       |     [.Sig Under Construction]       |
| Institut fur Theoretische Chemie     |   	        		     |
| Universitat Wien                     |                                     |
| Wahringerstrasse 17                  |                                     |
| 1090 Wien, Austria                   |    Ivo.Hofacker at itc.univie.ac.at    |
+--------------------------------------+-------------------------------------+




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