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Nucleic Acids Research Advance Access published online on May 3, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm258
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows

Jens Reeder, Peter Steffen and Robert Giegerich*

Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany

To whom correspondance should be addressed. Tel: +49 521 106 2913; Fax: +49 521 - 106 - 6411; Email: robert{at}techfak.uni-bielefeld.de

Received January 30, 2007. Revised March 28, 2007. Accepted April 8, 2007.

RNA pseudoknots are an important structural feature of RNAs, but often neglected in computer predictions for reasons of efficiency. Here, we present the pknotsRG Web Server 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 improved in several ways recently. First, it has been reimplemented in the C programming language, resulting in a 60-fold increase in speed. Second, 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. pknotsRG is available at the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/pknotsrg).


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[Abstract] [Full Text] [PDF]


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