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Multiple EM For Motif Elicitation
Multiple Expectation maximizations for Motif Elicitation (MEME) is a tool for discovering motifs in a group of related DNA or protein sequences.Bailey T.L., Elkan C. Unsupervised Learning of Multiple Motifs In Biopolymers Using EM. Mach. Learn. 1995;21:51–80. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences and is often associated with some biological function. MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of DNA or protein sequences (the training set) and outputs as many motifs as requested. It uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif. MEME is the first of a collecti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residue ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Motif
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue''. Overview When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein. Nevertheless, motifs need not be associated with a distinctive secondary structure. " Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). Outside of gene exons, there exist regulatory sequence motifs and motifs within the " junk", such as satellite DNA. Some of these are believed to affect the shape of nucleic acids (see for example RN ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Position Weight Matrix
A position weight matrix (PWM), also known as a position-specific weight matrix (PSWM) or position-specific scoring matrix (PSSM), is a commonly used representation of motifs (patterns) in biological sequences. PWMs are often derived from a set of aligned sequences that are thought to be functionally related and have become an important part of many software tools for computational motif discovery. Background Creation Conversion of sequence to position probability matrix A PWM has one row for each symbol of the alphabet (4 rows for nucleotides in DNA sequences or 20 rows for amino acids in protein sequences) and one column for each position in the pattern. In the first step in constructing a PWM, a basic position frequency matrix (PFM) is created by counting the occurrences of each nucleotide at each position. From the PFM, a position probability matrix (PPM) can now be created by dividing that former nucleotide count at each position by the number of sequences, thereb ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MEME Suite
The MEME suite is a collection of tools for the discovery and analysis of sequence motifs. Motif discovery MEME Multiple Expectation maximizations for Motif Elicitation (MEME) is a tool for discovering motifs in a group of related DNA or protein sequences. MEME takes as input a group of DNA or protein sequences and outputs as many motifs as requested up to a user-specified statistical confidence threshold. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif. GLAM2 Gapped local alignment of motifs (GLAM 2) is a tool for discovering gapped motifs in a group of DNA or protein sequences. Unlike MEME, GLAM2 does not try to find several different motifs all in one go. Instead, it performs replicates: it tries to find the best possible motif multiple times. DREME Discriminative Regular Expression Motif Elicitation (DREME) is a tool for discovering motifs in large collections of sequences. DREME is comp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Expectation Maximization
Expectation or Expectations may refer to: Science * Expectation (epistemic) * Expected value, in mathematical probability theory * Expectation value (quantum mechanics) * Expectation–maximization algorithm, in statistics Music * ''Expectation'' (album), a 2013 album by Girl's Day * ''Expectation'', a 2006 album by Matt Harding * ''Expectations'' (Keith Jarrett album), 1971 * ''Expectations'' (Dance Exponents album), 1985 * ''Expectations'' (Hayley Kiyoko album), 2018 **"Expectations/Overture", a song from the album * ''Expectations'' (Bebe Rexha album), 2018 * ''Expectations'' (Katie Pruitt album), 2020 **"Expectations", a song from the album * "Expectation" (waltz), a 1980 waltz composed by Ilya Herold Lavrentievich Kittler * "Expectation" (song), a 2010 song by Tame Impala * "Expectations" (song), a 2018 song by Lauren Jauregui * "Expectations", a song by Three Days Grace from ''Transit of Venus'', 2012 See also *''Great Expectations'', a novel by Charles Dickens *''X ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maximum Likelihood
In statistics, maximum likelihood estimation (MLE) is a method of estimation theory, estimating the Statistical parameter, parameters of an assumed probability distribution, given some observed data. This is achieved by Mathematical optimization, maximizing a likelihood function so that, under the assumed statistical model, the Realization (probability), observed data is most probable. The point estimate, point in the parameter space that maximizes the likelihood function is called the maximum likelihood estimate. The logic of maximum likelihood is both intuitive and flexible, and as such the method has become a dominant means of statistical inference. If the likelihood function is Differentiable function, differentiable, the derivative test for finding maxima can be applied. In some cases, the first-order conditions of the likelihood function can be solved analytically; for instance, the ordinary least squares estimator for a linear regression model maximizes the likelihood when ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Greedy Search
A greedy algorithm is any algorithm that follows the problem-solving heuristic of making the locally optimal choice at each stage. In many problems, a greedy strategy does not produce an optimal solution, but a greedy heuristic can yield locally optimal solutions that approximate a globally optimal solution in a reasonable amount of time. For example, a greedy strategy for the travelling salesman problem (which is of high computational complexity) is the following heuristic: "At each step of the journey, visit the nearest unvisited city." This heuristic does not intend to find the best solution, but it terminates in a reasonable number of steps; finding an optimal solution to such a complex problem typically requires unreasonably many steps. In mathematical optimization, greedy algorithms optimally solve combinatorial problems having the properties of matroids and give constant-factor approximations to optimization problems with the submodular structure. Specifics Greedy algorith ... [...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, 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. Sequence alignments are also used for non-biological sequences, such as calculating the distance cost between strings in a natural language or in 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 alignments of proteins, the degree of similarity between amino acids occupying a parti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
