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Bioinformatics Advance Access originally published online on December 20, 2005
Bioinformatics 2006 22(5):614-615; 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

Local RNA base pairing probabilities in large sequences

Stephan H. Bernhart 1, Ivo L. Hofacker 1,* and Peter F. Stadler 1,2,3

1Institut für Theoretische Chemie, Universität Wien Währingerstr. 17, A-1090 Wien, Austria
2Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig Härtelstr. 16-18, D-04107 Leipzig, Germany
3Santa Fe Institute 1399 Hyde Park Road, Santa Fe, NM 87501, USA

*To whom correspondence should be addressed.

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/

Contact: ivo{at}tbi.univie.ac.at

Received on October 30, 2005; revised on December 15, 2005; accepted on December 15, 2005

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