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Nucleic Acids Research, 2001, Vol. 29, No. 22 4724-4735
© 2001 Oxford University Press

RNAMotif, an RNA secondary structure definition and search algorithm

Thomas J. Macke1, David J. Ecker, Robin R. Gutell2, Daniel Gautheret3, David A. Case1 and Rangarajan Sampath*

Ibis Therapeutics, 2292 Faraday Avenue, Carlsbad, CA 92008, USA, 1Department of Molecular Biology, The Scripps Research Institute, San Diego, CA 92037, USA, 2 Institute for Cellular and Molecular Biology, Section of Integrative Biology, University of Texas, Austin, TX 78712, USA and 3CNRS UMR 6102/INSERM U 136, Luminy Case 906, 13288 Marseilles, France

RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural motifs will therefore enhance our understanding of RNA structure and help associate elements of RNA structure with functional and regulatory elements. Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif search algorithm, RNAMotif, and demonstrate its utility with some motif search examples. RNAMotif differs from other motif search tools in two important aspects: first, the structure definition language is more flexible and can specify any type of base–base interaction; second, RNAMotif provides a user controlled scoring section that can be used to add capabilities that patterns alone cannot provide.

* To whom correspondence should be addressed. Tel: +1 760 603 2652; Fax: +1 760 431 2768; Email: rsampath{at}isisph.com


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