Systematic and exhaustive RNA motif identification and classification is crucial for integration of RNA structural and sequence data. New methods are described for finding recurrent three –dimensional (3D) motifs in RNA atomic–resolution structures [1, 2]. Find RNA 3D (FR3D) is a suite of Matlab programs that implement geometric, symbolic, or mixed search. The goal of RNA 3D motif searching is to find and rank candidate motifs according to how closely they resemble the structure of the query motif. The inputs include a query motif in the form of a list of m nucleotides from a particular RNA 3D structure file, a set of RNA 3D structure files to search, and a cutoff discrepancy D0. The output is a list of candidate motifs from these structure files, sorted according to the geometric discrepancy between the candidate and query motifs [3]. We used FR3D for annotations of sarcin/ricin motif in the 50S ribosomal subunit in Haloarcula Marismortui, PDB (Protein Data Bank) files 3G4S, 3G6E, and 3CXC [4]. Geometric, symbolic, or mixed representations of RNA structure have been implemented in FR3D. The complete sarcin/ricin motif has nine nucleotides, which we used a six–nucleotide core sarcin/ricin submotif as the query motif. The geometric, symbolic, and mixed searches were conducted with discrepancy cutoff D0 set to 0.5. We found specify the relationships between these six bases in FR3D as follows that G2701/A2694 - trans Hoogsteen/suger-edage, A2702/U2693 - trans Watson-crick/Hoogsteen and A2703/A2691 - trans Hoogsteen/Hoogsteen in the query motif.

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