Publications - Published papers

Please find below publications of our group. Currently, we list 501 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Local RNA Base Pairing Probabilities in Large Sequences

Stephan Bernhart, Ivo L. Hofacker, Peter F. Stadler


PREPRINT 05-024: [ PDF ]  [ PS ]
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Bioinformatics 22: 614-615 (2006).


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.


RNA secondary structure, folding algorithms, base pairing probabilities


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