5mer

A 5-mer refers to a sequence or block of five units in a biological context. In nucleic acids, a 5-mer is a pentanucleotide, a sequence of five nucleotides (A, C, G, T in DNA; A, C, G, U in RNA). In proteins, the analogous term is a pentapeptide, a sequence of five amino acids. In genomics and proteomics, 5-mers are commonly treated as a type of k-mer, where k equals 5.

In DNA or RNA, there are 4^5 = 1024 possible 5-mers when using the standard bases. These short sequences are used in various computational analyses, including k-mer counting, error correction in sequencing reads, and the construction of de Bruijn graphs for genome assembly. 5-mer frequencies can aid in motif discovery, genome annotation, and studies of sequence composition or methylation contexts in epigenetics.

In proteins, a 5-mer or pentapeptide consists of five consecutive amino acids. With 20 standard amino acids, there are 20^5 = 3,200,000 possible pentapeptides. Such short motifs are examined in motif analysis, protein design, and studies of local structure or binding sites, though their brevity often limits specificity and increases combinatorial diversity.

Common tools and approaches for 5-mer analysis include specialized software for fast counting and memory-efficient storage, such as Jellyfish, KMC, and related de Bruijn graph-based methods. Researchers also apply 5-mer analyses to compare sequences across species, assess sequencing quality, and identify characteristic short motifs.

See also: k-mer, pentapeptide, de Bruijn graph.