pknotsRG -- tool for folding RNA secondary structures
What you can do:
RNA pseudoknot folding including near-optimal structures and sliding windows.
Highlights:
- The pknotsRG Web Server is for single sequence RNA secondary structure prediction including pseudoknots.
- pknotsRG employs the newest Turner energy rules for finding the structure of minimal free energy.
- The algorithm has been reimplemented in the C programming language, resulting in a 60-fold increase in speed.
- All suboptimal foldings up to a user-defined threshold can be enumerated.
- For large scale analysis, a fast sliding window mode is available.
- Further improvements of the Web Server are a new output visualization using the PseudoViewer Web Service or RNAmovies for a movie like animation of several suboptimal foldings.
- The tool is available as source code, binary executable, online tool or as Web Service.
- The latter alternative allows for an easy integration into bio-informatics pipelines.
Keywords:
- Nucleic Acid Conformation
- RNA
- pseudoknot
- RNA secondary structure prediction
Literature & Tutorials:
This record last updated: 06-04-2008