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Nucleic Acids Research Advance Access published online on April 22, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm222
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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 Paper

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

Andreas R. Gruber, Richard Neuböck, Ivo L. Hofacker and Stefan Washietl*

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria

*To whom correspondence should be addressed. Tel: +43-1-4277-52744; Fax: +43-1-4277-52793; Email: wash{at}tbi.univie.ac.at

Received January 29, 2007. Revised March 20, 2007. Accepted March 28, 2007.

Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of thermodynamic stability and evolutionary conservation. We present a web server that uses the RNAz algorithm to detect functional RNA structures in multiple alignments of nucleotide sequences. The server provides access to a complete and fully automatic analysis pipeline that allows not only to analyze single alignments in a variety of formats, but also to conduct complex screens of large genomic regions. Results are presented on a website that is illustrated by various structure representations and can be downloaded for local view. The web server is available at: rna.tbi.univie.ac.at/RNAz.


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