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Double Cut And Join Model
The double cut and join (DCJ) model is a model for genome rearrangement used to define an edit distance between genomes based on gene order and orientation, rather than nucleotide sequence. It takes the fundamental units of a genome to be synteny blocks, maximal sections of DNA conserved between genomes. It focuses on changes due to genome rearrangement operations such as inversions, translocations as well as the creation and absorption of circular intermediates. A genome is described as a directed, edge labeled graph with each vertex having degree 1 or 2. Edges are labeled as synteny blocks, vertices of degree 1 represent telomeres, and vertices of degree 2 representing adjacencies between blocks. This requires that the genome consist of cycles and paths. Each component is called a chromosome. The beginning of each edge is called the tail, the end of each edge is called the head; together heads and tails are known as extremities. Vertices are described by their roles as h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DCJ Example Genome
Drum Corps Japan (DCJ) is the administering organization for drum and bugle corps in Japan. Previously held indoors, most DCJ competitions are now held outdoors, similar to those in DCI. Competition scoring Competition scoring in the DCJ circuit is divided into three categories: ''music'', ''visual'', and ''effect''. Each of these categories is further broken into two sections. ''Music'' scores are divided into a ''brass'' caption score and a ''percussion'' caption score and reflect the level of musical execution by corps members. The two scores are added together to give the corps' overall music score. ''Visual'' scores are divided into a ''color guard'' caption score and a ''performance'' score and reflect the level of movement execution by corps members. The totals in these two categories are similarly added together for a corps' overall visual score. ''Effect'' scores reflect the overall impact of the show, both musically and visually. Both ''musical effect'' and ''visual ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Edit Distance
In computational linguistics and computer science, edit distance is a string metric, i.e. a way of quantifying how dissimilar two String (computing), strings (e.g., words) are to one another, that is measured by counting the minimum number of operations required to transform one string into the other. Edit distances find applications in natural language processing, where automatic Spell checker, spelling correction can determine candidate corrections for a misspelled word by selecting words from a dictionary that have a low distance to the word in question. In bioinformatics, it can be used to quantify the similarity of DNA sequences, which can be viewed as strings of the letters A, C, G and T. Different definitions of an edit distance use different sets of like operations. Levenshtein distance operations are the removal, insertion, or substitution of a character in the string. Being the most common metric, the term ''Levenshtein distance'' is often used interchangeably with ''edit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Synteny
In genetics, the term synteny refers to two related concepts: * In classical genetics, ''synteny'' describes the physical co-localization of genetic loci on the same chromosome within an individual or species. * In current biology, ''synteny'' more commonly refers to ''colinearity'', i.e. conservation of blocks of order within two sets of chromosomes that are being compared with each other. These blocks are referred to as ''syntenic blocks''. The Encyclopædia Britannica gives the following description of synteny, using the modern definition: Etymology ''Synteny'' is a neologism meaning "on the same ribbon"; Greek: ', ''syn'' "along with" + ', ''tainiā'' "band". This can be interpreted classically as "on the same chromosome", or in the modern sense of having the same order of genes on two (homologous) strings of DNA (or chromosomes). : co-localization on a chromosome The classical concept is related to genetic linkage: Linkage between two loci is established by the observat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromosomal Inversion
An inversion is a chromosome rearrangement in which a segment of a chromosome becomes inverted within its original position. An inversion occurs when a chromosome undergoes a two breaks within the chromosomal arm, and the segment between the two breaks inserts itself in the opposite direction in the same chromosome arm. The breakpoints of inversions often happen in regions of repetitive nucleotides, and the regions may be reused in other inversions. Chromosomal segments in inversions can be as small as 1 kilobases or as large as 100 megabases. The number of genes captured by an inversion can range from a handful of genes to hundreds of genes. Inversions can happen either through ectopic recombination between Repeated sequence (DNA), repetitive sequences, or through chromosomal breakage followed by non-homologous end joining. Inversions are of two types: paracentric inversion, paracentric and pericentric inversion, pericentric. Paracentric inversions do not include the centromere, a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromosomal Translocation
In genetics, chromosome translocation is a phenomenon that results in unusual rearrangement of chromosomes. This includes "balanced" and "unbalanced" translocation, with three main types: "reciprocal", "nonreciprocal" and "Robertsonian" translocation. Reciprocal translocation is a chromosome abnormality caused by exchange of parts between non-homologous chromosomes. Two detached fragments of two different chromosomes are switched. Robertsonian translocation occurs when two non-homologous chromosomes get attached, meaning that given two healthy pairs of chromosomes, one of each pair "sticks" and blends together homogeneously. Each type of chromosomal translocation can result in disorders for growth, function and the development of an individuals body, often resulting from a change in their genome. A gene fusion may be created when the translocation joins two otherwise-separated genes. It is detected on cytogenetics or a karyotype of affected cells. Translocations can be bala ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Richard M
Richard is a male given name. It originates, via Old French, from Frankish language, Old Frankish and is a Compound (linguistics), compound of the words descending from Proto-Germanic language, Proto-Germanic ''*rīk-'' 'ruler, leader, king' and ''*hardu-'' 'strong, brave, hardy', and it therefore means 'strong in rule'. Nicknames include "Richie", "Dick (nickname), Dick", "Dickon", "Dickie (name), Dickie", "Rich (given name), Rich", "Rick (given name), Rick", "Rico (name), Rico", "Ricky (given name), Ricky", and more. Richard is a common English (the name was introduced into England by the Normans), German and French male name. It's also used in many more languages, particularly Germanic, such as Norwegian, Danish, Swedish, Icelandic, and Dutch, as well as other languages including Irish, Scottish, Welsh and Finnish. Richard is cognate with variants of the name in other European languages, such as the Swedish "Rickard", the Portuguese and Spanish "Ricardo" and the Italian "Ricc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graph (discrete Mathematics)
In discrete mathematics, particularly in graph theory, a graph is a structure consisting of a Set (mathematics), set of objects where some pairs of the objects are in some sense "related". The objects are represented by abstractions called ''Vertex (graph theory), vertices'' (also called ''nodes'' or ''points'') and each of the related pairs of vertices is called an ''edge'' (also called ''link'' or ''line''). Typically, a graph is depicted in diagrammatic form as a set of dots or circles for the vertices, joined by lines or curves for the edges. The edges may be directed or undirected. For example, if the vertices represent people at a party, and there is an edge between two people if they shake hands, then this graph is undirected because any person ''A'' can shake hands with a person ''B'' only if ''B'' also shakes hands with ''A''. In contrast, if an edge from a person ''A'' to a person ''B'' means that ''A'' owes money to ''B'', then this graph is directed, because owing mon ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Telomeres
A telomere (; ) is a region of repetitive nucleotide sequences associated with specialized proteins at the ends of linear chromosomes (see Sequences). Telomeres are a widespread genetic feature most commonly found in eukaryotes. In most, if not all species possessing them, they protect the terminal regions of chromosomal DNA from progressive degradation and ensure the integrity of linear chromosomes by preventing DNA repair systems from mistaking the very ends of the DNA strand for a double-strand break. Discovery The existence of a special structure at the ends of chromosomes was independently proposed in 1938 by Hermann Joseph Muller, studying the fruit fly ''Drosophila melanogaster'', and in 1939 by Barbara McClintock, working with maize. Muller observed that the ends of irradiated fruit fly chromosomes did not present alterations such as deletions or inversions. He hypothesized the presence of a protective cap, which he coined "telomeres", from the Greek ''telos'' (end) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cycle (graph Theory)
In graph theory, a cycle in a graph is a non-empty trail in which only the first and last vertices are equal. A directed cycle in a directed graph is a non-empty directed trail in which only the first and last vertices are equal. A graph without cycles is called an ''acyclic graph''. A directed graph without directed cycles is called a '' directed acyclic graph''. A connected graph without cycles is called a ''tree''. Definitions Circuit and cycle * A circuit is a non-empty trail in which the first and last vertices are equal (''closed trail''). : Let be a graph. A circuit is a non-empty trail with a vertex sequence . * A cycle or simple circuit is a circuit in which only the first and last vertices are equal. * ''n'' is called the length of the circuit resp. length of the cycle. Directed circuit and directed cycle * A directed circuit is a non-empty directed trail in which the first and last vertices are equal (''closed directed trail''). : Let be a directed grap ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Path (graph Theory)
In graph theory, a path in a graph is a finite or infinite sequence of edges which joins a sequence of vertices which, by most definitions, are all distinct (and since the vertices are distinct, so are the edges). A directed path (sometimes called dipath) in a directed graph is a finite or infinite sequence of edges which joins a sequence of distinct vertices, but with the added restriction that the edges be all directed in the same direction. Paths are fundamental concepts of graph theory, described in the introductory sections of most graph theory texts. See e.g. , , or . cover more advanced algorithmic topics concerning paths in graphs. Definitions Walk, trail, and path * A walk is a finite or infinite sequence of edges which joins a sequence of vertices. : Let be a graph. A finite walk is a sequence of edges for which there is a sequence of vertices such that ''Φ''(''e''''i'') = for . is the ''vertex sequence'' of the walk. The walk is ''closed'' if ''v''1 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metric Space
In mathematics, a metric space is a Set (mathematics), set together with a notion of ''distance'' between its Element (mathematics), elements, usually called point (geometry), points. The distance is measured by a function (mathematics), function called a metric or distance function. Metric spaces are a general setting for studying many of the concepts of mathematical analysis and geometry. The most familiar example of a metric space is 3-dimensional Euclidean space with its usual notion of distance. Other well-known examples are a sphere equipped with the angular distance and the hyperbolic plane. A metric may correspond to a Conceptual metaphor , metaphorical, rather than physical, notion of distance: for example, the set of 100-character Unicode strings can be equipped with the Hamming distance, which measures the number of characters that need to be changed to get from one string to another. Since they are very general, metric spaces are a tool used in many different bra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
