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mmsearch: a motif arrangement language and search program

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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. 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.

Normal distribution

In statistics, a normal distribution or Gaussian distribution is a type of continuous probability distribution for a real-valued random variable. The general form of its probability density function is The parameter is the mean or expectation of the distribution (and also its median and mode), while the parameter is its standard deviation. The variance of the distribution is . A random variable with a Gaussian distribution is said to be normally distributed, and is called a normal deviate.

Cauchy distribution

The Cauchy distribution, named after Augustin Cauchy, is a continuous probability distribution. It is also known, especially among physicists, as the Lorentz distribution (after Hendrik Lorentz), Cauchy–Lorentz distribution, Lorentz(ian) function, or Breit–Wigner distribution. The Cauchy distribution is the distribution of the x-intercept of a ray issuing from with a uniformly distributed angle. It is also the distribution of the ratio of two independent normally distributed random variables with mean zero.

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.

Language death

In linguistics, language death occurs when a language loses its last native speaker. By extension, language extinction is when the language is no longer known, including by second-language speakers, when it becomes known as an extinct language. A related term is linguicide, the death of a language from natural or political causes, and, rarely, glottophagy, the absorption or replacement of a minor language by a major language.

Language

Language is a structured system of communication that consists of grammar and vocabulary. It is the primary means by which humans convey meaning, both in spoken and written forms, and may also be conveyed through sign languages. The vast majority of human languages have developed writing systems that allow for the recording and preservation of the sounds or signs of language. Human language is characterized by its cultural and historical diversity, with significant variations observed between cultures and across time.

Stable distribution

In probability theory, a distribution is said to be stable if a linear combination of two independent random variables with this distribution has the same distribution, up to location and scale parameters. A random variable is said to be stable if its distribution is stable. The stable distribution family is also sometimes referred to as the Lévy alpha-stable distribution, after Paul Lévy, the first mathematician to have studied it. Of the four parameters defining the family, most attention has been focused on the stability parameter, (see panel).

F-distribution

In probability theory and statistics, the F-distribution or F-ratio, also known as Snedecor's F distribution or the Fisher–Snedecor distribution (after Ronald Fisher and George W. Snedecor), is a continuous probability distribution that arises frequently as the null distribution of a test statistic, most notably in the analysis of variance (ANOVA) and other F-tests. The F-distribution with d1 and d2 degrees of freedom is the distribution of where and are independent random variables with chi-square distributions with respective degrees of freedom and .

Extinct language

An extinct language is a language that no longer has any speakers, especially if the language has no living descendants. In contrast, a dead language is one that is no longer the native language of any community, even if it is still in use, like Latin. A dormant language is a dead language that still serves as a symbol of ethnic identity to a particular group. These languages are often undergoing a process of revitalisation. Languages that currently have living native speakers are sometimes called modern languages to contrast them with dead languages, especially in educational contexts.

Ratio distribution

A ratio distribution (also known as a quotient distribution) is a probability distribution constructed as the distribution of the ratio of random variables having two other known distributions. Given two (usually independent) random variables X and Y, the distribution of the random variable Z that is formed as the ratio Z = X/Y is a ratio distribution. An example is the Cauchy distribution (also called the normal ratio distribution), which comes about as the ratio of two normally distributed variables with zero mean.