Suffix Techniques as a Rapid Method for RNA Substructure Search

Raphael A. Bauer[1,2] (
Kristian Rother[3,4] (
Janusz M. Bujnicki[3,4] (
Robert Preissner[1] (

[1] Institute of Molecular Biology and Bioinformatics, Structural Bioinformatics Group, Charité Universitätsmedizin (Medical University), Arnimallee 22, 14195 Berlin, Germany
[2] Graduate School: Genomics and Systems Biology of Molecular Networks, Monbijoustr. 2, 10117 Berlin, Germany
[3] International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
[4] Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland


The RNA Ontology Consortium recently proposed a two-letter representation of the RNA backbone conformation. In this study, we compare the suite notation to a custom string representation that utilizes η -θ pseudotorsion angles. Both representations were used to assess similarity and self-similarity in several RNA structure datasets. For the detection of similarities between two RNA structures we are utilizing suffix techniques that allow for the detection of substructure similarity within some degree of inexactness. The suite representation as well as the pseudotorsion representation was tested on four diverse RNA datasets. The possibility to detect structural similarities on these datasets allowed to recover many homologous structural elements that have implications for further understanding of the RNA apparatus in Systems Biology. The software as well as the utilized datasets are freely available from

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Japanese Society for Bioinformatics