MC-Search: a three-dimensional RNA pattern matching tool Martin Larose, Patrick Gendron and...

MC-Search: a three-dimensional RNA pattern matching tool

Martin Larose, Patrick Gendron and François Major

Département d'informatique et de recherche opérationnelleUniversité de Montréal, Montréal, Québec, Canada

Poster #356

MC-Tools

MC-Core 01(library)

MC-RMS

MC-Search 04 MC-Annotate 01MC-Sym 91

RNA graph(descriptor)

3D Structures

Classes

3D StructureDatabase

Annotated3D 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.