Consensus sequence

In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated sequence of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It represents the results of multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. Such information is important when considering sequence-dependent enzymes such as RNA polymerase.

To address the limitations of consensus sequences—which reduce variability to a single residue per position—sequence logos provide a richer visual representation of aligned sequences. Logos display each position as a stack of letters (nucleotides or amino acids), where the height of a letter corresponds to its frequency in the alignment, and the total stack height reflects the information content (measured in bits). The most frequent residue appears at the top of the stack, preserving the consensus while also revealing subtle patterns, such as functionally important but less frequent residues (e.g., alternative start codons or transcription factor binding sites).