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Dot Plot (bioinformatics)
In bioinformatics a dot plot is a graphical method for comparing two biological sequences and identifying regions of close similarity after sequence alignment. It is a type of recurrence plot. History One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes. For a simple visual representation of the similarity between two sequences, individual cells in the matrix can be shaded black if residues are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix. Interpretation Some idea of the similarity of the two sequences can be gleaned from the number and length of matching segments shown in the matrix. Identical proteins will obviously have a diagonal line in the center of the matrix. I ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence (biology)
A sequence in biology is the one-dimensional ordering of monomers, covalently linked within a biopolymer; it is also referred to as the primary structure of a biological macromolecule. While it can refer to many different molecules, the term sequence is most often used to refer to a DNA sequence or a protein sequence.https://www.nobelprize.org/uploads/2018/06/sanger-lecture.pdf See also * Dot plot (bioinformatics) * Sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome ... References Molecular biology {{molecular-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Alignment
In 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 biology, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix (mathematics), matrix. Gaps are inserted between the Residue (chemistry), residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences such as calculating the Edit distance, distance cost between strings in a natural language, or to display financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence ali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Recurrence Plot
In descriptive statistics and chaos theory, a recurrence plot (RP) is a plot showing, for each moment j in time, the times at which the state of a dynamical system returns to the previous state at i, i.e., when the phase space trajectory visits roughly the same area in the phase space as at time j. In other words, it is a plot of :\vec(i)\approx \vec(j), showing i on a horizontal axis and j on a vertical axis, where \vec is the state of the system (or its phase space trajectory). Background Natural processes can have a distinct recurrent behaviour, e.g. periodicities (as seasonal or Milankovich cycles), but also irregular cyclicities (as El Niño Southern Oscillation, heart beat intervals). Moreover, the recurrence of states, in the meaning that states are again arbitrarily close after some time of divergence, is a fundamental property of deterministic dynamical systems and is typical for nonlinear or chaotic systems (cf. Poincaré recurrence theorem). The recurrence of states ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Residue (chemistry)
In chemistry, residue is whatever remains or acts as a contaminant after a given class of events. Residue may be the material remaining after a process of preparation, separation, or purification, such as distillation, evaporation, or filtration. It may also denote the undesired by-products of a chemical reaction. Residues as an undesired by-product are a concern in agricultural and food industries. Food safety Toxic chemical residues, wastes or contamination from other processes, are a concern in food safety. The most common food residues originate from pesticides, veterinary drugs, and industrial chemicals. For example, the U.S. Food and Drug Administration (FDA) and the Canadian Food Inspection Agency (CFIA) have guidelines for detecting chemical residues that are possibly dangerous to consume. In the U.S., the FDA is responsible for setting guidelines while other organizations enforce them. Environmental concerns Similar to the food industry, in environmental science ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tuple
In mathematics, a tuple is a finite sequence or ''ordered list'' of numbers or, more generally, mathematical objects, which are called the ''elements'' of the tuple. An -tuple is a tuple of elements, where is a non-negative integer. There is only one 0-tuple, called the ''empty tuple''. A 1-tuple and a 2-tuple are commonly called a singleton and an ordered pair, respectively. The term ''"infinite tuple"'' is occasionally used for ''"infinite sequences"''. Tuples are usually written by listing the elements within parentheses "" and separated by commas; for example, denotes a 5-tuple. Other types of brackets are sometimes used, although they may have a different meaning. An -tuple can be formally defined as the image of a function that has the set of the first natural numbers as its domain. Tuples may be also defined from ordered pairs by a recurrence starting from an ordered pair; indeed, an -tuple can be identified with the ordered pair of its first elements and its t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Direct Relationship
In mathematics, two sequences of numbers, often experimental data, are proportional or directly proportional if their corresponding elements have a constant ratio. The ratio is called ''coefficient of proportionality'' (or ''proportionality constant'') and its reciprocal is known as ''constant of normalization'' (or ''normalizing constant''). Two sequences are inversely proportional if corresponding elements have a constant product. Two functions f(x) and g(x) are ''proportional'' if their ratio \frac is a constant function. If several pairs of variables share the same direct proportionality constant, the equation expressing the equality of these ratios is called a proportion, e.g., (for details see Ratio). Proportionality is closely related to ''linearity''. Direct proportionality Given an independent variable ''x'' and a dependent variable ''y'', ''y'' is directly proportional to ''x'' if there is a positive constant ''k'' such that: : y = kx The relation is often ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Contact Map
A protein contact map represents the distance between all possible Amino acid, amino acid residue pairs of a three-dimensional protein structure using a binary two-dimensional Matrix (mathematics), matrix. For two residues i and j, the ij element of the matrix is 1 if the two residues are closer than a predetermined threshold, and 0 otherwise. Various contact definitions have been proposed: The distance between the Cα-Cα atom with threshold 6-12 Ångström, Å; distance between Cβ-Cβ atoms with threshold 6-12 Å (Cα is used for Glycine); and distance between the side-chain Center of mass, centers of mass. Overview Contact maps provide a more reduced representation of a protein structure than its full 3D atomic coordinates. The advantage is that contact maps are invariant to rotations and translations. They are more easily predicted by machine learning methods. It has also been shown that under certain circumstances (e.g. low content of erroneously predicted contacts) it is poss ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Recurrence Plot
In descriptive statistics and chaos theory, a recurrence plot (RP) is a plot showing, for each moment j in time, the times at which the state of a dynamical system returns to the previous state at i, i.e., when the phase space trajectory visits roughly the same area in the phase space as at time j. In other words, it is a plot of :\vec(i)\approx \vec(j), showing i on a horizontal axis and j on a vertical axis, where \vec is the state of the system (or its phase space trajectory). Background Natural processes can have a distinct recurrent behaviour, e.g. periodicities (as seasonal or Milankovich cycles), but also irregular cyclicities (as El Niño Southern Oscillation, heart beat intervals). Moreover, the recurrence of states, in the meaning that states are again arbitrarily close after some time of divergence, is a fundamental property of deterministic dynamical systems and is typical for nonlinear or chaotic systems (cf. Poincaré recurrence theorem). The recurrence of states ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Self-similarity Matrix
In data analysis, the self-similarity matrix is a graphical representation of similar sequences in a data series. Similarity can be explained by different measures, like spatial distance ( distance matrix), correlation, or comparison of local histograms or spectral properties (e.g. IXEGRAM). A similarity plot can be the starting point for dot plots or recurrence plots. Definition To construct a self-similarity matrix, one first transforms a data series into an ordered sequence of feature vectors V = (v_1, v_2, \ldots, v_n) , where each vector v_i describes the relevant features of a data series in a given local interval. Then the self-similarity matrix is formed by computing the similarity of pairs of feature vectors : S(j,k) = s(v_j, v_k) \quad j,k \in (1,\ldots,n) where s(v_j, v_k) is a function measuring the similarity of the two vectors, for instance, the inner product s(v_j, v_k) = v_j \cdot v_k. Then similar segments of feature vectors will show up as path of high s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
