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Genomic distances under deletions and insertions

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Polynomial

In mathematics, a polynomial is an expression consisting of indeterminates (also called variables) and coefficients, that involves only the operations of addition, subtraction, multiplication, and positive-integer powers of variables. An example of a polynomial of a single indeterminate x is x2 − 4x + 7. An example with three indeterminates is x3 + 2xyz2 − yz + 1. Polynomials appear in many areas of mathematics and science.

Human genome

The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs.

Reference genome

A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized individual organism of a species. As they are assembled from the sequencing of DNA from a number of individual donors, reference genomes do not accurately represent the set of genes of any single individual organism. Instead a reference provides a haploid mosaic of different DNA sequences from each donor.

Permutation matrix

In mathematics, particularly in matrix theory, a permutation matrix is a square binary matrix that has exactly one entry of 1 in each row and each column and 0s elsewhere. Each such matrix, say P, represents a permutation of m elements and, when used to multiply another matrix, say A, results in permuting the rows (when pre-multiplying, to form PA) or columns (when post-multiplying, to form AP) of the matrix A.

Polynomial ring

In mathematics, especially in the field of algebra, a polynomial ring or polynomial algebra is a ring (which is also a commutative algebra) formed from the set of polynomials in one or more indeterminates (traditionally also called variables) with coefficients in another ring, often a field. Often, the term "polynomial ring" refers implicitly to the special case of a polynomial ring in one indeterminate over a field. The importance of such polynomial rings relies on the high number of properties that they have in common with the ring of the integers.

Levenshtein distance

In information theory, linguistics, and computer science, the Levenshtein distance is a string metric for measuring the difference between two sequences. Informally, the Levenshtein distance between two words is the minimum number of single-character edits (insertions, deletions or substitutions) required to change one word into the other. It is named after the Soviet mathematician Vladimir Levenshtein, who considered this distance in 1965.

Present value

In economics and finance, present value (PV), also known as present discounted value, is the value of an expected income stream determined as of the date of valuation. The present value is usually less than the future value because money has interest-earning potential, a characteristic referred to as the time value of money, except during times of zero- or negative interest rates, when the present value will be equal or more than the future value. Time value can be described with the simplified phrase, "A dollar today is worth more than a dollar tomorrow".

Metagenomics

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample.

Approximation error

The approximation error in a data value is the discrepancy between an exact value and some approximation to it. This error can be expressed as an absolute error (the numerical amount of the discrepancy) or as a relative error (the absolute error divided by the data value). An approximation error can occur for a variety of reasons, among them a computing machine precision or measurement error (e.g. the length of a piece of paper is 4.53 cm but the ruler only allows you to estimate it to the nearest 0.

Mathematical logic

Mathematical logic is the study of formal logic within mathematics. Major subareas include model theory, proof theory, set theory, and recursion theory (also known as computability theory). Research in mathematical logic commonly addresses the mathematical properties of formal systems of logic such as their expressive or deductive power. However, it can also include uses of logic to characterize correct mathematical reasoning or to establish foundations of mathematics.