Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 05-024

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Titel:
Local Base Pairing Probabilities in Large RNAs

Author(s):
Stephan Bernhart, Ivo L. Hofacker, Peter F. Stadler,

Submitted
Bioinformatics

Abstract:
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.

Keywords: RNA secondary structure, folding algorithms, base pairing probabilities


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