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Nucleic Acids Research, 2001, Vol. 29, No. 1 196-198
© 2001 Oxford University Press

HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns

Stefan Gräf, Dirk Strothmann1, Stefan Kurtz1 and Gerhard Steger*

Institut für Physikalische Biologie, Geb 26.12.U1, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany and 1Technische Fakultät, Universität Bielefeld, Germany

The database, called HyPaLib (for Hybrid Pattern Library), contains annotated structural elements characteristic for certain classes of structural and/or functional RNAs. These elements are described in a language specifically designed for this purpose. The language allows convenient specification of hybrid patterns, i.e. motifs consisting of sequence features and structural elements together with sequence similarity and thermodynamic constraints. We are currently developing software tools that allow a user to search sequence databases for any pattern in HyPaLib, thus providing functionality which is similar to PROSITE, but dedicated to the more complex patterns in RNA sequences. HyPaLib is available at http://bibiserv.techfak.uni-bielefeld.de/HyPa/.

* To whom correspondence should be addressed. Tel: +49 211 81 14927; Fax: +49 211 81 15167; Email: steger{at}biophys.uni-duesseldorf.de


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