Local RNA base pairing probabilities in large sequences.

Stephan H Bernhart; Ivo L Hofacker; Peter F Stadler

doi:10.1093/bioinformatics/btk014

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Local RNA base pairing probabilities in large sequences.

Stephan H Bernhart·Ivo L Hofacker·Peter F Stadler

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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/.

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Algorithms Base Pairing Chromosome Mapping Computer Simulation Models, Genetic Models, Statistical RNA Sequence Alignment Sequence Analysis, RNA Software Journal Article Research Support, Non-U.S. Gov't

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BibTeX RIS

Stephan H Bernhart, Ivo L Hofacker, Peter F Stadler. 2005-12-20. Local RNA base pairing probabilities in large sequences.. https://doi.org/10.1093/bioinformatics%2Fbtk014

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