Sequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Graph enumerationIn combinatorics, an area of mathematics, graph enumeration describes a class of combinatorial enumeration problems in which one must count undirected or directed graphs of certain types, typically as a function of the number of vertices of the graph. These problems may be solved either exactly (as an algebraic enumeration problem) or asymptotically. The pioneers in this area of mathematics were George Pólya, Arthur Cayley and J. Howard Redfield.
Independent set (graph theory)In graph theory, an independent set, stable set, coclique or anticlique is a set of vertices in a graph, no two of which are adjacent. That is, it is a set of vertices such that for every two vertices in , there is no edge connecting the two. Equivalently, each edge in the graph has at most one endpoint in . A set is independent if and only if it is a clique in the graph's complement. The size of an independent set is the number of vertices it contains. Independent sets have also been called "internally stable sets", of which "stable set" is a shortening.
Split graphIn graph theory, a branch of mathematics, a split graph is a graph in which the vertices can be partitioned into a clique and an independent set. Split graphs were first studied by , and independently introduced by . A split graph may have more than one partition into a clique and an independent set; for instance, the path a–b–c is a split graph, the vertices of which can be partitioned in three different ways: the clique {a, b} and the independent set {c} the clique {b, c} and the independent set {a} the clique {b} and the independent set {a, c} Split graphs can be characterized in terms of their forbidden induced subgraphs: a graph is split if and only if no induced subgraph is a cycle on four or five vertices, or a pair of disjoint edges (the complement of a 4-cycle).
Graph isomorphismIn graph theory, an isomorphism of graphs G and H is a bijection between the vertex sets of G and H such that any two vertices u and v of G are adjacent in G if and only if and are adjacent in H. This kind of bijection is commonly described as "edge-preserving bijection", in accordance with the general notion of isomorphism being a structure-preserving bijection. If an isomorphism exists between two graphs, then the graphs are called isomorphic and denoted as . In the case when the bijection is a mapping of a graph onto itself, i.
Planar graphIn graph theory, a planar graph is a graph that can be embedded in the plane, i.e., it can be drawn on the plane in such a way that its edges intersect only at their endpoints. In other words, it can be drawn in such a way that no edges cross each other. Such a drawing is called a plane graph or planar embedding of the graph. A plane graph can be defined as a planar graph with a mapping from every node to a point on a plane, and from every edge to a plane curve on that plane, such that the extreme points of each curve are the points mapped from its end nodes, and all curves are disjoint except on their extreme points.
Rooted graphIn mathematics, and, in particular, in graph theory, a rooted graph is a graph in which one vertex has been distinguished as the root. Both directed and undirected versions of rooted graphs have been studied, and there are also variant definitions that allow multiple roots. Rooted graphs may also be known (depending on their application) as pointed graphs or flow graphs. In some of the applications of these graphs, there is an additional requirement that the whole graph be reachable from the root vertex.
Maximal independent setIn graph theory, a maximal independent set (MIS) or maximal stable set is an independent set that is not a subset of any other independent set. In other words, there is no vertex outside the independent set that may join it because it is maximal with respect to the independent set property. For example, in the graph P_3, a path with three vertices a, b, and c, and two edges and , the sets {b} and {a, c} are both maximally independent. The set {a} is independent, but is not maximal independent, because it is a subset of the larger independent set {a, c}.
Vertex separatorIn graph theory, a vertex subset S \subset V is a vertex separator (or vertex cut, separating set) for nonadjacent vertices a and b if the removal of S from the graph separates a and b into distinct connected components. Consider a grid graph with r rows and c columns; the total number n of vertices is r × c. For instance, in the illustration, r = 5, c = 8, and n = 40. If r is odd, there is a single central row, and otherwise there are two rows equally close to the center; similarly, if c is odd, there is a single central column, and otherwise there are two columns equally close to the center.
Partial cubeIn graph theory, a partial cube is a graph that is isometric to a subgraph of a hypercube. In other words, a partial cube can be identified with a subgraph of a hypercube in such a way that the distance between any two vertices in the partial cube is the same as the distance between those vertices in the hypercube. Equivalently, a partial cube is a graph whose vertices can be labeled with bit strings of equal length in such a way that the distance between two vertices in the graph is equal to the Hamming distance between their labels.
