Nucleic Acids Research Advance Access published online on October 4, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl692
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Methods Online |
Structural analysis of aligned RNAs
Experimental Bioinformatics, Institute of Biology II, Freiburg University, Schänzlestrasse 1 79104 Freiburg, Germany
To whom correspondence should be addressed. Tel: +49 761 203 6975; Fax: +49 761 203 2601; Email: bjoern.voss{at}biologie.uni-freiburg.de
Received June 16, 2006. Revised September 7, 2006. Accepted September 7, 2006.
The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de.