Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German Conference on Bioinformatics 2004, GCB 2004, October 4-6, 2004, Bielefeld, Germany P-53, 207-216 (2004).

GI, Gesellschaft für Informatik, Bonn


Robert Giegerich (ed.), Jens Stoye (ed.)

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Conserved RNA pseudoknots

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


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 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.

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GI, Gesellschaft für Informatik, Bonn
ISBN 3-88579-382-2

Last changed 04.10.2013 18:03:59