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RNAspa is a comparative structure prediction program for a set of RNA sequences.
It does so by initially running RNAsubopt (a component of Vienna Package). Therefore, Vienna Package must be installed BEFORE running RNAspa.

Download the source code of RNAspa version 1.1, and the sample input file. The instructions can be found inside the source file.

Here is the supplementary information.

The authors of RNAspa are: Yair Horesh , Tirza Doniger , Shulamit Michaeli , and Ron Unger

And the full reference is:
Yair Horesh, Tirza Doniger, Shulamit Michaeli and Ron Unger, RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules, BMC Bioinformatics, vol. 8:366, 2007

Last update: 2/10/07