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.