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Nucleic Acids Research 2004 32(Web Server Issue):W154-W159; doi:10.1093/nar/gkh352
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

Riboswitch finder—a tool for identification of riboswitch RNAs

Peter Bengert1,2 and Thomas Dandekar1,2,3,4,*

1 Biochemiezentrum, Project Group B2 (Dandekar/Schirmer), University of Heidelberg, Im Neuenheimer Feld 504, 69120 Heidelberg, Germany, 2 Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, Germany, 3 EMBL, Postfach 102209, D-69012 Heidelberg, Germany and 4 Max Delbrueck Centre for Molecular Medicine, Robert-Roessle-Strabe 10, 13092 Berlin-Buch, Germany

* To whom correspondence should be addressed at Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, Germany. Tel: +49 931 888 4551; Fax: +49 931 888 4552; Email: dandekar{at}biozentrum.uni-wuerzburg.de

Received January 27, 2004; Revised and Accepted February 20, 2004

We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence elements and secondary structure, calculates and displays the energy folding of the RNA structure and runs a number of tests including this information to determine whether high-sensitivity riboswitch motifs (or variants) according to the Bacillus subtilis type are present in the given RNA sequence. Batch-mode determination (all sequences input at once and separated by FASTA format) is also possible. The program has been implemented and is available both as local software for in-house installation and as a web server at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/Riboswitch/.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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