Talk abstracts

Talk on Friday 02:10-02:30pm submitted by Jesse Stombaugh

FR3D: A Tool for Finding, Scoring and Clustering 3D Recurrent RNA Motifs

Jesse Stombaugh (Department of Biological Sciences, Bowling Green State University), Craig L. Zirbel (Department of Mathematics, Bowling Green State University), Neocles. B. Leontis (Department of Chemistry, Bowling Green State University)

Abstract:
The "Find RNA 3D" (FR3D) suite of programs exhaustively searches RNA atomic-resolution 3D structures for local and composite recurrent RNA 3D motifs, sets of RNA nucleotides with similar spatial arrangements. Local motifs comprise nucleotides in a single hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different strand segments. FR3D uses a base-centered approach to efficiently, yet exhaustive search with geometric, symbolic, or mixed representations of RNA structure. Each base is represented by the position of its geometric center in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and -stacking interactions are calculated from the base geometries and represented using Leontis/Westhof bp classification. These data are stored for motif searches. For geometric searches, a user-supplied 3D query motif is used to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain. A geometric discrepancy is defined to score and rank candidate motifs. Since it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs in the RNA database, a screening algorithm was devised that is guaranteed to find all motifs having discrepancy below a user-specified cut-off. Candidate motifs identified geometrically may be screened symbolically for particular basepair or stacking arrangement, sequence continuity or identity constraints. Purely symbolic searches for motifs containing user-defined sequence, continuity and interaction constraints have also been implemented. Post-processing facilities allow the user to organize the candidate motifs into clusters and to display a multiple alignment of the nucleotide sequence corresponding to each candidate. The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal computer in a matter of minutes. FR3D is available at: http://rna.bgsu.edu/FR3D.

Keywords: Recurrent Motifs, Structural Bioinformatics