Publications - Published papers

Please find below publications of our group. Currently, we list 508 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.

Prediction of Consensus RNA Secondary Structures Including Pseudoknots

Christina Witwer, Ivo L. Hofacker, Peter F. Stadler


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IEEE/ACM Trans.Comp.Biol.Bioinf. 1: 66-77 (2004).


Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to five different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly, and more than 85% of the base pairs were identified.


RNA secondary structure, pseudoknots, covariance scores.