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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. Inse ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...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. See also * Protein sequence * DNA sequence * Genotype * Self-incompatibility in plants * List of geneticists * Human Genome Project * Dot plot (bioinformatics) * Multiplex Ligation-dependent Probe Amplification * 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. Methodologies used include sequence alig ... 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, 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] |
Recurrence Plot
In descriptive statistics and chaos theory, a recurrence plot (RP) is a plot showing, for each moment i 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] |
Tuple
In mathematics, a tuple is a finite ordered list (sequence) of elements. An -tuple is a sequence (or ordered list) of elements, where is a non-negative integer. There is only one 0-tuple, referred to as ''the empty tuple''. An -tuple is defined inductively using the construction of an ordered pair. Mathematicians usually write tuples by listing the elements within parentheses "" and separated by a comma and a space; for example, denotes a 5-tuple. Sometimes other symbols are used to surround the elements, such as square brackets "nbsp; or angle brackets "⟨ ⟩". Braces "" are used to specify arrays in some programming languages but not in mathematical expressions, as they are the standard notation for sets. The term ''tuple'' can often occur when discussing other mathematical objects, such as vectors. In computer science, tuples come in many forms. Most typed functional programming languages implement tuples directly as product types, tightly associated with algebr ... [...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, which is called the coefficient of proportionality or proportionality constant. Two sequences are inversely proportional if corresponding elements have a constant product, also called the coefficient of proportionality. This definition is commonly extended to related varying quantities, which are often called ''variables''. This meaning of ''variable'' is not the common meaning of the term in mathematics (see variable (mathematics)); these two different concepts share the same name for historical reasons. 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 rela ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparative Genomics
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences (sequences that share a common ancestry) in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Contact Map
A protein contact map represents the distance between all possible amino acid residue pairs of a three-dimensional protein structure using a binary two-dimensional 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 Å; distance between Cβ-Cβ atoms with threshold 6-12 Å (Cα is used for Glycine); and distance between the side-chain 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 possible to reconstruct the 3D coordinates of a protein using it ... [...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 i 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). This technique is also applied for the search of a given pattern in a long data series as in gene matching. 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 pro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
