In cryptography, a cipher is an algorithm for performing encryption or decryption—a series of well-defined steps that can be followed as a procedure. An alternative, less common term is encipherment. To encipher or encode is to convert information into cipher or code. In common parlance, "cipher" is synonymous with "code", as they are both a set of steps that encrypt a message; however, the concepts are distinct in cryptography, especially classical cryptography.
An identifier is a name that identifies either a unique object or a unique class of objects, where the "object" or class may be an idea, physical countable object, or physical noncountable substance. The abbreviation ID often refers to identity, identification, or an identifier. An identifier may be a word, number, letter, symbol, or any combination of those.
A connotation is a commonly understood cultural or emotional association that any given word or phrase carries, in addition to its explicit or literal meaning, which is its denotation.
A synonym is a word, morpheme, or phrase that means exactly or nearly the same as another word, morpheme, or phrase in a given language. For example, in the English language, the words begin, start, commence, and initiate are all synonyms of one another: they are synonymous. The standard test for synonymy is substitution: one form can be replaced by another in a sentence without changing its meaning. Words are considered synonymous in only one particular sense: for example, long and extended in the context long time or extended time are synonymous, but long cannot be used in the phrase extended family. Synonyms with exactly the same meaning share a seme or denotational sememe, whereas those with inexactly similar meanings share a broader denotational or connotational sememe and thus overlap within a semantic field. The former are sometimes called cognitive synonyms and the latter, near-synonyms, plesionyms or poecilonyms.
The suffix -onym is a bound morpheme, that is attached to the end of a root word, thus forming a new compound word that designates a particular class of names. In linguistic terminology, compound words that are formed with suffix -onym are most commonly used as designations for various onomastic classes. Most onomastic terms that are formed with suffix -onym are classical compounds, whose word roots are taken from classical languages.
In genetics and bioinformatics, a single-nucleotide polymorphism is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population.
A code is a rule for converting a piece of information into another object or action, not necessarily of the same sort.
A synonymous substitution is the evolutionary substitution of one base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence is not modified. This is possible because the genetic code is "degenerate", meaning that some amino acids are coded for by more than one three-base-pair codon; since some of the codons for a given amino acid differ by just one base pair from others coding for the same amino acid, a mutation that replaces the "normal" base by one of the alternatives will result in incorporation of the same amino acid into the growing polypeptide chain when the gene is translated. Synonymous substitutions and mutations affecting noncoding DNA are often considered silent mutations; however, it is not always the case that the mutation is silent.
Black Code or Black Codes may refer to:
In genetics, the Ka/Ks ratio, also known as ω or dN/dS ratio, is used to estimate the balance between neutral mutations, purifying selection and beneficial mutations acting on a set of homologous protein-coding genes. It is calculated as the ratio of the number of nonsynonymous substitutions per non-synonymous site (Ka), in a given period of time, to the number of synonymous substitutions per synonymous site (Ks), in the same period. The latter are assumed to be neutral, so that the ratio indicates the net balance between deleterious and beneficial mutations. Values of Ka/Ks significantly above 1 are unlikely to occur without at least some of the mutations being advantageous. If beneficial mutations are assumed to make little contribution, then Ka/Ks estimates the degree of evolutionary constraint.
Neutral mutations are changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics, mutations in which natural selection does not affect the spread of the mutation in a species are termed neutral mutations. Neutral mutations that are inheritable and not linked to any genes under selection will be lost or will replace all other alleles of the gene. That loss or fixation of the gene proceeds based on random sampling known as genetic drift. A neutral mutation that is in linkage disequilibrium with other alleles that are under selection may proceed to loss or fixation via genetic hitchhiking and/or background selection.
Cohesion is the grammatical and lexical linking within a text or sentence that holds a text together and gives it meaning. It is related to the broader concept of coherence.
Cognitive synonymy is a type of synonymy in which synonyms are so similar in meaning that they cannot be differentiated either denotatively or connotatively, that is, not even by mental associations, connotations, emotive responses, and poetic value. It is a stricter technical definition of synonymy, specifically for theoretical purposes. In usage employing this definition, synonyms with greater differences are often called near-synonyms rather than synonyms.
A nonsynonymous substitution is a nucleotide mutation that alters the amino acid sequence of a protein. Nonsynonymous substitutions differ from synonymous substitutions, which do not alter amino acid sequences and are (sometimes) silent mutations. As nonsynonymous substitutions result in a biological change in the organism, they are subject to natural selection.
In databases, a synonym is an alias or alternate name for a table, view, sequence, or other schema object. They are used mainly to make it easy for users to access database objects owned by other users. They hide the underlying object's identity and make it harder for a malicious program or user to target the underlying object. Because a synonym is just an alternate name for an object, it requires no storage other than its definition. When an application uses a synonym, the DBMS forwards the request to the synonym's underlying base object. By coding your programs to use synonyms instead of database object names, you insulate yourself from any changes in the name, ownership, or object locations. If you frequently refer to a database object that has a long name, you might appreciate being able to refer to it with a shorter name without having to rename it and alter the code referring to it.
Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. It includes many sophisticated methods and tools for phylogenomics and phylomedicine. It is licensed as proprietary freeware. The project for developing this software was initiated by the leadership of Masatoshi Nei in his laboratory at the Pennsylvania State University in collaboration with his graduate student Sudhir Kumar and postdoctoral fellow Koichiro Tamura. Nei wrote a monograph (pp. 130) outlining the scope of the software and presenting new statistical methods that were included in MEGA. The entire set of computer programs was written by Kumar and Tamura. The personal computers then lacked the ability to send the monograph and software electronically, so they were delivered by postal mail. From the start, MEGA was intended to be easy-to-use and include solid statistical methods only.
The McDonald–Kreitman test is a statistical test often used by evolutionary and population biologists to detect and measure the amount of adaptive evolution within a species by determining whether adaptive evolution has occurred, and the proportion of substitutions that resulted from positive selection. To do this, the McDonald–Kreitman test compares the amount of variation within a species (polymorphism) to the divergence between species (substitutions) at two types of sites, neutral and nonneutral. A substitution refers to a nucleotide that is fixed within one species, but a different nucleotide is fixed within a second species at the same base pair of homologous DNA sequences. A site is nonneutral if it is either advantageous or deleterious. The two types of sites can be either synonymous or nonsynonymous within a protein-coding region. In a protein-coding sequence of DNA, a site is synonymous if a point mutation at that site would not change the amino acid, also known as a silent mutation. Because the mutation did not result in a change in the amino acid that was originally coded for by the protein-coding sequence, the phenotype, or the observable trait, of the organism is generally unchanged by the silent mutation. A site in a protein-coding sequence of DNA is nonsynonymous if a point mutation at that site results in a change in the amino acid, resulting in a change in the organism's phenotype. Typically, silent mutations in protein-coding regions are used as the "control" in the McDonald–Kreitman test.
Kukatj, also rendered Gugadj, is an extinct Paman language of the Cape York Peninsula, Queensland, Australia. The name Kalibamu has also been assigned to it, although this may be a separate dialect. It is spoken by the Kukatj people. A single speaker was last recorded in 1975.
Tcl is a high-level, general-purpose, interpreted, dynamic programming language. It was designed with the goal of being very simple but powerful. Tcl casts everything into the mold of a command, even programming constructs like variable assignment and procedure definition. Tcl supports multiple programming paradigms, including object-oriented, imperative, functional, and procedural styles.
