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Representative Sequences
In social sciences and other domains, representative sequences are whole sequences that best characterize or summarize a set of sequences. In bioinformatics, representative sequences also designate substrings of a sequence that characterize the sequence. Social sciences In Sequence analysis in social sciences, representative sequences are used to summarize sets of sequences describing for example the family life course or professional career of several thousands individuals. The identification of representative sequences proceeds from the pairwise dissimilarities between sequences. One typical solution is the medoid sequence, i.e., the observed sequence that minimizes the sum of its distances to all other sequences in the set. An other solution is the densest observed sequence, i.e., the sequence with the greatest number of other sequences in its neighborhood. When the diversity of the sequences is large, a single representative is often insufficient to efficiently characterize ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Analysis In Social Sciences
In social sciences, sequence analysis (SA) is concerned with the analysis of sets of categorical sequences that typically describe longitudinal data. Analyzed sequences are encoded representations of, for example, individual life trajectories such as family formation, school to work transitions, working careers, but they may also describe daily or weekly time use or represent the evolution of observed or self-reported health, of political behaviors, or the development stages of organizations. Such sequences are chronologically ordered unlike words or DNA sequences for example. SA is a longitudinal analysis approach that is holistic in the sense that it considers each sequence as a whole. SA is essentially exploratory. Broadly, SA provides a comprehensible overall picture of sets of sequences with the objective of characterizing the structure of the set of sequences, finding the salient characteristics of groups, identifying typical paths, comparing groups, and more generally studyin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Primary Structure
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences. Formation Biological Amino acids are polymerised via peptide bonds to form a long backbone, with the different amino acid side chains protruding along it. In biological systems, proteins are produced during translation by a cell's ribosomes. Some organisms can also make short peptides by non-ribosomal peptide synthesis, which often use amino acids other than the standard 20, and may be cyclised, modified and cross-linked. Chemical Peptides can be synthesised chemically via a range of laboratory methods. Chemical methods typically synthesise ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Evolution
Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes. History The history of molecular evolution starts in the early 20th century with comparative biochemistry, and the use of "fingerprinting" methods such as immune assays, gel electrophoresis and paper chromatography in the 1950s to explore homologous proteins. The field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular ... [...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 li ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Housekeeping Gene
In molecular biology, housekeeping genes are typically constitutive genes that are required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal and patho-physiological conditions. Although some housekeeping genes are expressed at relatively constant rates in most non-pathological situations, the expression of other housekeeping genes may vary depending on experimental conditions. The origin of the term "housekeeping gene" remains obscure. Literature from 1976 used the term to describe specifically tRNA and rRNA. For experimental purposes, the expression of one or multiple housekeeping genes is used as a reference point for the analysis of expression levels of other genes. The key criterion for the use of a housekeeping gene in this manner is that the chosen housekeeping gene is uniformly expressed with low variance under both control and experimental conditions. Validation of housekeeping genes should be performed before th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Orthologous
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene transfer event (xenologs). Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. Identity, similarity, and conservation The term "percent homology" is often used to mean "sequence similarity”, that is the percentage of identical residues (''percent identity''), or the percentage of residues conserved with similar physicochemical properties ('' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Distance Matrices In Phylogeny
Distance matrices are used in phylogeny as non-parametric distance methods and were originally applied to phenetic data using a matrix of pairwise distances. These distances are then reconciled to produce a tree (a phylogram, with informative branch lengths). The distance matrix can come from a number of different sources, including measured distance (for example from immunological studies) or morphometric analysis, various pairwise distance formulae (such as euclidean distance) applied to discrete morphological characters, or genetic distance from sequence, restriction fragment, or allozyme data. For phylogenetic character data, raw distance values can be calculated by simply counting the number of pairwise differences in character states (Hamming distance). Distance-matrix methods Distance-matrix methods of phylogenetic analysis explicitly rely on a measure of "genetic distance" between the sequences being classified, and therefore they require an MSA (multiple sequence alig ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Sequence
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences. Formation Biological Amino acids are polymerised via peptide bonds to form a long backbone, with the different amino acid side chains protruding along it. In biological systems, proteins are produced during translation by a cell's ribosomes. Some organisms can also make short peptides by non-ribosomal peptide synthesis, which often use amino acids other than the standard 20, and may be cyclised, modified and cross-linked. Chemical Peptides can be synthesised chemically via a range of laboratory methods. Chemical methods typically synthesise ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Function (biology)
In evolutionary biology, function is the reason some object or process occurred in a system that evolved through natural selection. That reason is typically that it achieves some result, such as that chlorophyll helps to capture the energy of sunlight in photosynthesis. Hence, the organism that contains it is more likely to survive and reproduce, in other words the function increases the organism's fitness. A characteristic that assists in evolution is called an adaptation; other characteristics may be non-functional spandrels, though these in turn may later be co-opted by evolution to serve new functions. In biology, function has been defined in many ways. In physiology, it is simply what an organ, tissue, cell or molecule does. In the philosophy of biology, talk of function inevitably suggests some kind of teleological purpose, even though natural selection operates without any goal for the future. All the same, biologists often use teleological language as a shorthand for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation tends to exist within any given population as a result of genetic mutation and recombination. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or more rare within a population. The evolutionary pressures that determine whether a characteristic is common or rare within a population constantly change, resulting in a change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms, and molecules. The theory of evolution by ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Domain
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins. Background The concept of the domain was first proposed in 1973 by Wetlaufer aft ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
