9mer

A 9-mer is any sequence consisting of nine consecutive elements. The term is a specific case of the general k-mer concept, where k denotes the sequence length. 9-mers can refer to nucleotide sequences in DNA or RNA, as well as to amino acid sequences in proteins. In sequence analysis, counting and examining 9-mers helps with tasks such as motif discovery, repetitive-element detection, and estimation of sequence complexity, since the frequency and distribution of length-9 substrings reflect underlying biological structure.

In immunology and proteomics, 9-mer peptides are particularly notable because nine amino acids is a common length for peptides presented by MHC class I molecules to CD8+ T cells. These nine-residue peptides, sometimes called nonamers, are frequently used in epitope discovery and vaccine design. Computational tools often predict binding of 9-mer peptides to specific HLA alleles, with certain positions acting as anchor residues that influence binding affinity. While many 9-mers are generated in a given protein, only a subset may function as effective epitopes.

Beyond biology, 9-mers appear in broader k-mer analyses of genomic data, where researchers examine all possible substrings of length nine within longer sequences to study sequence composition, error profiles, or comparative genomics across samples. The concept of a 9-mer therefore spans multiple disciplines, united by the simple idea of fixed-length subsequences of nine units.