k-mer

The term k-mer (or x-mer where x can be virtually any consonant of choice) usually refers to a specific n-tuple or n-gram of nucleic acid or amino acid sequences that can be used to identify certain regions within biomolecules like DNA (e.g. for gene prediction) 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 combinations (or rather permutations with repetitions) are used. Specific short k-mers are called oligomers or "oligos" for short.

Applications

• In algorithms for Sequence assembly
• In algorithms for Sequence alignment

See also

• polymer
• N-gram
• N-tuple
• lattice models

Examples

• A sequence of dimers = AGAGAGAGAGAGAG
• A sequence of trimers = AAGAAGAAGAAG

External links

• Lattice models for protein-DNA binding