Suffix techniques as a rapid method for RNA substructure search.

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 eta - theta 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 http://suiterna.sourceforge.net.