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Bioinformatics Advance Access published online on December 20, 2005
Bioinformatics, doi:10.1093/bioinformatics/btk014
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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 30, 2005
Revised December 15, 2005
Accepted December 15, 2005

Applications note

Local RNA base pairing probabilities in large sequences

Stephan H. Bernhart 1, Ivo L. Hofacker 1 *, and Peter F. Stadler 2

1 Institut für Theoretische Chemie, Universität Wien, Währingerstr. 17, A-1090 Wien, Austria
2 Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany; Institut für Theoretische Chemie, Universität Wien, Währingerstr. 17, A-1090 Wien, Austria; Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501

* To whom correspondence should be addressed.
Ivo L. Hofacker, E-mail: ivo{at}tbi.univie.ac.at


  Abstract

Summary: The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically unknown, arbitrary sequence windows have to be used in practice. Here we present a method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window.

Availability: The program RNAplfold is part of the Vienna RNA Package and can be downloaded from http://www.tbi.univie.ac.at/RNA/.


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