Local RNA base pairing probabilities in large sequences

Authors:
Stephan H. Bernhart;Ivo L. Hofacker;Peter F. Stadler
Affiliations:
Institut für Theoretische Chemie, Universität Wien Währingerstr. 17, A-1090 Wien, Austria;Institut für Theoretische Chemie, Universität Wien Währingerstr. 17, A-1090 Wien, Austria;Institut für Theoretische Chemie, Universität Wien Währingerstr. 17, A-1090 Wien, Austria
Venue:
Bioinformatics
Year:
2006

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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/ Contact: ivo@tbi.univie.ac.at