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Direct Coupling Analysis
Direct coupling analysis or DCA is an umbrella term comprising several methods for analyzing sequence data in computational biology. The common idea of these methods is to use statistical modeling to quantify the strength of the direct relationship between two positions of a biological sequence, excluding effects from other positions. This contrasts usual measures of correlation, which can be large even if there is no direct relationship between the positions (hence the name ''direct'' coupling analysis). Such a direct relationship can for example be the evolutionary pressure for two positions to maintain mutual compatibility in the biomolecular structure of the sequence, leading to molecular coevolution between the two positions. DCA has been used in the inference of protein residue contacts, RNA structure prediction, the inference of protein-protein interaction networks, the modeling of fitness landscapes, and the identification of functionally relevant residue communities. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Biology
Computational biology refers to the use of data analysis, mathematical modeling and Computer simulation, computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer engineering which uses bioengineering to build computers. History Bioinformatics, the analysis of informatics processes in biological systems, began in the early 1970s. At this time, research in artificial intelligence was using network models of the human brain in order to generate new algorithms. This use of biological data pushed biological researchers to use computers to evaluate and compare large data sets in their own field. By 1982, researchers shared information via Punched card, punch cards. The amount of data grew exponentially by the end of the 1980s, requiring new computational method ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha amino acids appear in the genetic code. Amino acids can be classified according to the locations of the core structural functional groups, as Alpha and beta carbon, alpha- , beta- , gamma- or delta- amino acids; other categories relate to Chemical polarity, polarity, ionization, and side chain group type (aliphatic, Open-chain compound, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid '' residues'' form the second-largest component (water being the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling l ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multiple Sequence Alignment
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino aci ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mutual Information
In probability theory and information theory, the mutual information (MI) of two random variables is a measure of the mutual dependence between the two variables. More specifically, it quantifies the " amount of information" (in units such as shannons (bits), nats or hartleys) obtained about one random variable by observing the other random variable. The concept of mutual information is intimately linked to that of entropy of a random variable, a fundamental notion in information theory that quantifies the expected "amount of information" held in a random variable. Not limited to real-valued random variables and linear dependence like the correlation coefficient, MI is more general and determines how different the joint distribution of the pair (X,Y) is from the product of the marginal distributions of X and Y. MI is the expected value of the pointwise mutual information (PMI). The quantity was defined and analyzed by Claude Shannon in his landmark paper "A Mathemati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lagrange Multiplier
In mathematical optimization, the method of Lagrange multipliers is a strategy for finding the local maxima and minima of a function subject to equality constraints (i.e., subject to the condition that one or more equations have to be satisfied exactly by the chosen values of the variables). It is named after the mathematician Joseph-Louis Lagrange. The basic idea is to convert a constrained problem into a form such that the derivative test of an unconstrained problem can still be applied. The relationship between the gradient of the function and gradients of the constraints rather naturally leads to a reformulation of the original problem, known as the Lagrangian function. The method can be summarized as follows: in order to find the maximum or minimum of a function f(x) subjected to the equality constraint g(x) = 0, form the Lagrangian function :\mathcal(x, \lambda) = f(x) + \lambda g(x) and find the stationary points of \mathcal considered as a function of x and the Lagrange m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Shannon Entropy
Shannon may refer to: People * Shannon (given name) * Shannon (surname) * Shannon (American singer), stage name of singer Shannon Brenda Greene (born 1958) * Shannon (South Korean singer), British-South Korean singer and actress Shannon Arrum Williams (born 1998) * Shannon, intermittent stage name of English singer-songwriter Marty Wilde (born 1939) * Claude Shannon (1916-2001) was American mathematician, electrical engineer, and cryptographer known as a "father of information theory" Places Australia * Shannon, Tasmania, a locality * Hundred of Shannon, a cadastral unit in South Australia * Shannon, a former name for the area named Calomba, South Australia since 1916 * Shannon River (Western Australia) Canada * Shannon, New Brunswick, a community * Shannon, Quebec, a city * Shannon Bay, former name of Darrell Bay, British Columbia * Shannon Falls, a waterfall in British Columbia Ireland * River Shannon, the longest river in Ireland ** Shannon Cave, a subterranean section ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Covariance
In probability theory and statistics, covariance is a measure of the joint variability of two random variables. If the greater values of one variable mainly correspond with the greater values of the other variable, and the same holds for the lesser values (that is, the variables tend to show similar behavior), the covariance is positive. In the opposite case, when the greater values of one variable mainly correspond to the lesser values of the other, (that is, the variables tend to show opposite behavior), the covariance is negative. The sign of the covariance therefore shows the tendency in the linear relationship between the variables. The magnitude of the covariance is not easy to interpret because it is not normalized and hence depends on the magnitudes of the variables. The normalized version of the covariance, the correlation coefficient, however, shows by its magnitude the strength of the linear relation. A distinction must be made between (1) the covariance of two ra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Principle Of Maximum Entropy
The principle of maximum entropy states that the probability distribution which best represents the current state of knowledge about a system is the one with largest entropy, in the context of precisely stated prior data (such as a proposition that expresses testable information). Another way of stating this: Take precisely stated prior data or testable information about a probability distribution function. Consider the set of all trial probability distributions that would encode the prior data. According to this principle, the distribution with maximal information entropy is the best choice. History The principle was first expounded by E. T. Jaynes in two papers in 1957 where he emphasized a natural correspondence between statistical mechanics and information theory. In particular, Jaynes offered a new and very general rationale why the Gibbsian method of statistical mechanics works. He argued that the entropy of statistical mechanics and the information entropy of infor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Matrix Norm
In mathematics, a matrix norm is a vector norm in a vector space whose elements (vectors) are matrices (of given dimensions). Preliminaries Given a field K of either real or complex numbers, let K^ be the -vector space of matrices with m rows and n columns and entries in the field K. A matrix norm is a norm on K^. This article will always write such norms with double vertical bars (like so: \, A\, ). Thus, the matrix norm is a function \, \cdot\, : K^ \to \R that must satisfy the following properties: For all scalars \alpha \in K and matrices A, B \in K^, *\, A\, \ge 0 (''positive-valued'') *\, A\, = 0 \iff A=0_ (''definite'') *\left\, \alpha A\right\, =\left, \alpha\ \left\, A\right\, (''absolutely homogeneous'') *\, A+B\, \le \, A\, +\, B\, (''sub-additive'' or satisfying the ''triangle inequality'') The only feature distinguishing matrices from rearranged vectors is multiplication. Matrix norms are particularly useful if they are also sub-multiplicative: *\le ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Prior Distribution
In Bayesian statistical inference, a prior probability distribution, often simply called the prior, of an uncertain quantity is the probability distribution that would express one's beliefs about this quantity before some evidence is taken into account. For example, the prior could be the probability distribution representing the relative proportions of voters who will vote for a particular politician in a future election. The unknown quantity may be a parameter of the model or a latent variable rather than an observable variable. Bayes' theorem calculates the renormalized pointwise product of the prior and the likelihood function, to produce the '' posterior probability distribution'', which is the conditional distribution of the uncertain quantity given the data. Similarly, the prior probability of a random event or an uncertain proposition is the unconditional probability that is assigned before any relevant evidence is taken into account. Priors can be created using a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Likelihood Function
The likelihood function (often simply called the likelihood) represents the probability of random variable realizations conditional on particular values of the statistical parameters. Thus, when evaluated on a given sample, the likelihood function indicates which parameter values are more ''likely'' than others, in the sense that they would have made the observed data more probable. Consequently, the likelihood is often written as \mathcal(\theta\mid X) instead of P(X \mid \theta), to emphasize that it is to be understood as a function of the parameters \theta instead of the random variable X. In maximum likelihood estimation, the arg max of the likelihood function serves as a point estimate for \theta, while local curvature (approximated by the likelihood's Hessian matrix) indicates the estimate's precision. Meanwhile in Bayesian statistics, parameter estimates are derived from the converse of the likelihood, the so-called posterior probability, which is calculated via Baye ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Potts Model
In statistical mechanics, the Potts model, a generalization of the Ising model, is a model of interacting spins on a crystalline lattice. By studying the Potts model, one may gain insight into the behaviour of ferromagnets and certain other phenomena of solid-state physics. The strength of the Potts model is not so much that it models these physical systems well; it is rather that the one-dimensional case is exactly solvable, and that it has a rich mathematical formulation that has been studied extensively. The model is named after Renfrey Potts, who described the model near the end of his 1951 Ph.D. thesis. The model was related to the "planar Potts" or " clock model", which was suggested to him by his advisor, Cyril Domb. The four-state Potts model is sometimes known as the Ashkin–Teller model, after Julius Ashkin and Edward Teller, who considered an equivalent model in 1943. The Potts model is related to, and generalized by, several other models, including the XY model, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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