In bioinformatics, k-mers are substrings of length contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed of nucleotides (i.e. A, T, G, and C), k-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines. Usually, the term k-mer refers to all of a sequence's subsequences of length , such that the sequence AGAT would have four monomers (A, G, A, and T), three 2-mers (AG, GA, AT), two 3-mers (AGA and GAT) and one 4-mer (AGAT). More generally, a sequence of length will have k-mers and there exist total possible k-mers, where is number of possible monomers (e.g. four in the case of DNA).
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K-mer in the context of N-gram
An n-gram is a sequence of n adjacent symbols in a particular order. The symbols may be n adjacent letters (including punctuation marks and blanks), syllables, or rarely whole words found in a language dataset; or adjacent phonemes extracted from a speech-recording dataset, or adjacent base pairs extracted from a genome. They are collected from a text corpus or speech corpus.
If Latin numerical prefixes are used, then n-gram of size 1 is called a "unigram", size 2 a "bigram" (or, less commonly, a "digram") etc. If, instead of the Latin ones, the English cardinal numbers are furtherly used, then they are called "four-gram", "five-gram", etc. Similarly, Greek numerical prefixes such as "monomer", "dimer", "trimer", "tetramer", "pentamer", etc., or English cardinal numbers, "one-mer", "two-mer", "three-mer", etc. are used in computational biology for polymers or oligomers of a known size, called k-mers. When the items are words, n-grams may also be called shingles.
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