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Bioinformatics Advance Access published online on December 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/btk010
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 25, 2005
Revised December 13, 2005
Accepted December 14, 2005

Applications note

RNAshapes: an integrated RNA analysis package based on abstract shapes

Peter Steffen 1 *, Björn Voß 2, Marc Rehmsmeier 3, Jens Reeder 1, and Robert Giegerich 1

1 Faculty of Technology, Bielefeld University, 33594 Bielefeld, Germany
2 Institute of Biology II, Experimental Bioinformatics, Freiburg University, Schänzlestr. 1, 79104 Freiburg, Germany
3 Center for Biotechnology (CeBiTec), Bielefeld University, 33594 Bielefeld, Germany

* To whom correspondence should be addressed.
Peter Steffen, E-mail: psteffen{at}techfak.uni-bielefeld.de


  Abstract

Summary: We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities, and the consensus shapes approach. This new package is completely reimplemented in C, and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching, and a sliding window approach.

Availability: RNAshapes is freely available at http://bibiserv.techfak.uni-bielefeld.de/rnashapes/ as C source code, and as compiled binaries for the most common computer architectures. For Microsoft Windows, we also offer a graphical user interface with convenient access to the complete functionality of the package.


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