In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology|structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix (mathematics)|matrix. Gaps are inserted between the Residue (chemistry)|residues so that identical or similar characters are aligned in successive columns.
Key: Single letters: Amino acid#Table of standard amino acid abbreviations and side chain properties|amino acids. Red: small, hydrophobic, aromatic, not Y. Blue: acidic. Magenta: basic. Green: hydroxyl, amine, amide, basic. Gray: others. *: identical. :: conserved substitutions (same colour group). .: semi-conserved substitution (similar shapes).
Sequence alignments are also used for non-biological sequences, such as those present in natural language or in financial data.