### RAG Glossary

adjacency matrix: a square matrix specifying the connectivity of a graph.

bridge graph: a graph with at least one edge whose deletion results in a disconnected graph.

bulge: mismatched base pairs in a helical stem other than a loop or a junction.

connected graph: every pair of vertices in a connected graph has a path from one vertex to another.

ct file: file containing data about the base pairs in an RNA secondary structure.

diagonal matrix: a square matrix that identifies the number of connections each vertex makes along the diagonal of the matrix

digraph or directed graph: a graph each of whose edge has a specified direction.

disconnected graph: a graph with two or more subgraphs that are not connected.

dual graph: a general graphical representation for RNA secondary structures.

edge: an edge in a graph is a line (possibly curved) joining two vertices or points.

hairpin loop: unmatched bases in single-strand turn region of a helical stem.

isomorphic graphs: graphs that are structurally equivalent.

internal loop: mismatched base pairs in a helical stem.

in vitro selection: an experimental method for selecting novel functional RNAs from a pool of sequences.

junction: three or more helical stems converging to form a closed structure.

kissing hairpins: hairpin loops in close proximity with complementary bases.

laplacian eigenvalues: eigenvalues calculated from the Laplacian matrix (second eigenvalue specifies the compactness of the graph)

laplacian matrix: a mathematical representation of the connectivity between the vertices in an RNA graph or topology.

planar tree graph: a 2D representation of a tree network.

pseudoknot: complex 3D motif involving intertwining of strand segments (a topology in which a stretch of nucleotides within a hairpin loop pairs with nucleotides external to that loop)

RNA tree: an RNA having tree-like branching structures with no pseudoknots.

stem: a motif in the secondary structure that represents more than one complementary base pair

vertex: a vertex in a graph is a point or node where lines (edges) originate or end.

Page | by Dr. Radut