MC-Search: a three-dimensional RNA pattern matching tool Martin Larose, Patrick Gendron and François Major Département d'informatique et de recherche opérationnelle.

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MC-Search: a three-dimensional RNA pattern matching tool Martin Larose, Patrick Gendron and François Major Département d'informatique et de recherche opérationnelle Université de Montréal, Montréal, Québec, Canada Poster #356

MC-Tools MC-Core 01 (library) MC-RMS MC-Search 04MC-Annotate 01MC-Sym 91 RNA graph (descriptor) 3D Structures Classes 3D Structure Database Annotated 3D Structure Database (RNA graphs) MC-Cycles 05

MC-Search aim Establish the relation between a RNA pattern and its 3-D structure. Two applications: Precise the definition of the pattern when looking for it in genomic sequences. Simplify RNA 3-D modeling by dividing the RNA in 3-D fragments that can be assembled in complete RNA models.

MC-Search Ontology (RNA graph / Descriptor) The nomenclature or vocabulary of the input employs simple RNA structure terms taken from the universe of discourse of the RNA structure experts. Each term must refer to precise and unambiguous RNA sequence, geometrical and stereochemical features that can be verified computationally. The class and subclass relations are formally and unambiguously defined.

GNRA Ontology When we say "GNRA tetraloops", what do we mean? When we say "GNRA fold", what do we mean? Questions that come to mind: "Do they include a flanking Watson-Crick base pair?“ "Are Watson-Crick base pairs limited to GC, AU?“ "Is the GNRA fold limited to hairpin loops?“

A Strict Descriptor of the GNRA tetraloop N R G A

GNRA Pattern Generalization N R G A

Generalized GNRA Occurrences in 1JJ2 26 fragments Three subclasses according to the presence/absence of covalent linkages. All but between R and A (red) Between G and N, N and R, and R and A (green) All but between N and R (blue). GNRA tetraloops at the tip of canonical stems are in the green cluster, but are not limited to the GNRA sequence.