Publications - Published papers

Please find below publications of our group. Currently, we list 500 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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Conserved RNA Pseudoknots

Caroline Thurner, Ivo L. Hofacker, Peter F. Stadler


PREPRINT 04-010: [ PDF ]  [ PS ]
[ Publishers's page ]


In: Robert Giegerich and Jens Stoye (eds), German Conference on Bioinformatics 2004, pp.207-216 (2004) [GI-Edition; Lecture Notes in Informatics Vol. P-53].


Pseudoknots are essential for the functioning of many small RNA molecules. In addition, viral RNAs often exhibit pseudoknots that are required at various stages of the viral life-cycle. Techniques for detecting evolutionarily conserved, and hence most likely functional RNA pseudoknots, are therefore of interest. Here we present an extension of the \texttt{alidot} approach that extracts conserved secondary structures from a multiple sequence alignment and predicted secondary structures of the individual sequences. In contrast to purely phylogenetic methods, this approach yields good results already for small samples of 10 sequences or even less.


conserved RNA structures, pseudoknots