The term k-mer usually refers to a specific n-tuple or n-gram

N-gram

In the fields of computational linguistics and probability, an n-gram is a contiguous sequence of n items from a given sequence of text or speech. The items in question can be phonemes, syllables, letters, words or base pairs according to the application...

 of nucleic acid

Nucleic acid

Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...

 or amino acid

Amino acid

Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

 sequence

Sequence

In mathematics, a sequence is an ordered list of objects . Like a set, it contains members , and the number of terms is called the length of the sequence. Unlike a set, order matters, and exactly the same elements can appear multiple times at different positions in the sequence...

s that can be used to identify certain regions within biomolecules like DNA

DNA

Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 (e.g. for gene prediction

Gene prediction

In computational biology gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functional elements such as regulatory regions...

) or proteins. Either k-mer strings as such can be used for finding regions of interest, or k-mer statistics giving discrete probability distributions of a number of possible k-mer combination

Combination

In mathematics a combination is a way of selecting several things out of a larger group, where order does not matter. In smaller cases it is possible to count the number of combinations...

s (or rather permutation

Permutation

In mathematics, the notion of permutation is used with several slightly different meanings, all related to the act of permuting objects or values. Informally, a permutation of a set of objects is an arrangement of those objects into a particular order...

s with repetitions) are used. Specific short k-mers are called oligomer

Oligomer

In chemistry, an oligomer is a molecule that consists of a few monomer units , in contrast to a polymer that, at least in principle, consists of an unlimited number of monomers. Dimers, trimers, and tetramers are oligomers. Many oils are oligomeric, such as liquid paraffin...

s or "oligos" for short.

External links

• Lattice models for protein-DNA binding