### 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.