Poster #356
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
MC-Tools
MC-Core 01
(library)
RNA graph
(descriptor)
MC-Sym 91
3D Structure
Database
MC-Search 04
3D Structures
MC-RMS
Classes
MC-Cycles 05
MC-Annotate 01
Annotated
3D Structure
Database
(RNA graphs)
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
G
R
A
GNRA Pattern Generalization
N
G
R
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.