Publications - Published papers

Please find below publications of our group. Currently, we list 456 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:

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A Folding Algorithm for Extended RNA Secondary Structures

Christian Höner zu Siederdissen, Stephan H. Bernhart, Peter F. Stadler, Ivo L. Hofacker

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Bioinformatics (2011) 27 (13): i129-i136

Abstract


Motivation:<br> RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment.<br> Results:<br> We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction.<br> Availability:<br> All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at <a href="www.tbi.univie.ac.at/~choener/segfold/"><tt>www.tbi.univie.ac.at/~choener/segfold/</tt></a>

Keywords


RNA secondary structure, non-canonical base pairs, RNA structure prediction