pknotsRG -- tool for folding RNA secondary structures

URL:
http://bibiserv.techfak.uni-bielefeld.de/pknotsrg
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:
PubMed Link: pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
This record last updated: 06-04-2008
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