The oldest and still most important field in RNA bioinformatics is predicting RNA secondary structures. The Vienna package is a set of command-line tools for basic tasks, like:
- RNAfold – predicts the 2D structure from a RNA sequence with the lowest energy using the Zuker algorithm.
- RNAsubopt – predicts several suboptimal 2D structures from a sequence.
- RNAalifold – folds two or more aligned RNA sequences.
- RNAup – predict RNA-RNA interactions.
.. and many more.
Each of these tools is well-tested, well-documented, and freely available – and has been for many years. To make their usage easier, the developers have created the Vienna RNA Websuite, a web interface for all the programs. With it, anyone new to the field can easily explore what these tools can do to RNA sequences.
The entire Vienna package and web server is available at: http://rna.tbi.univie.ac.at/.
Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA websuite. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W70-4. Epub 2008 Apr 19. PMID: 18424795
