k-mer

In bioinformatics, k-mers are substrings of length ${\displaystyle k}$ 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 ${\displaystyle k}$, 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 ${\displaystyle L}$ will have ${\displaystyle L-k+1}$ k-mers and ${\displaystyle n^{k}}$ total possible k-mers, where ${\displaystyle n}$ is number of possible monomers (e.g. four in the case of DNA).