Local RNA base pairing probabilities in large sequences

Stephan H Bernhart; Ivo L Hofacker; Peter F Stadler

doi:10.1093/bioinformatics/btk014

Local RNA base pairing probabilities in large sequences

Bioinformatics. 2006 Mar 1;22(5):614-5. doi: 10.1093/bioinformatics/btk014. Epub 2005 Dec 20.

Authors

Stephan H Bernhart¹, Ivo L Hofacker, Peter F Stadler

Affiliation

¹ Institut für Theoretische Chemie, Universität Wien, Währingerstr. 17, A-1090 Wien, Austria.

PMID: 16368769
DOI: 10.1093/bioinformatics/btk014

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/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Base Pairing / genetics*
Chromosome Mapping / methods*
Computer Simulation
Models, Genetic*
Models, Statistical
RNA / chemistry*
RNA / genetics*
Sequence Alignment / methods*
Sequence Analysis, RNA / methods*
Software*

Substances

RNA