Sequence alignment

Sequence alignment arranges DNA, RNA, or protein sequences so corresponding positions, substitutions, insertions, and deletions can be compared.

Substitution matrix: A table assigning scores to substitutions between symbols, often amino acids, in a sequence alignment. It rewards biologically plausible residue matches, such as conservative amino-acid substitutions.
DNA: A nucleic acid that stores hereditary information in most organisms. DNA sequences are commonly aligned to compare genes and genomes.
Multiple sequence alignment: An arrangement of three or more biological sequences that aligns corresponding positions across them. It reveals patterns conserved across a group rather than a single pair.
Global alignment: An alignment that matches two sequences across their full lengths. It suits sequences expected to correspond from end to end.
Gap penalty: A score cost imposed for introducing gaps into an alignment. Its size controls how readily an alignment explains insertions and deletions.
RNA: A nucleic acid involved in gene expression, regulation, and other cellular functions. RNA alignments compare transcripts and conserved functional regions.
Sequence homology search: A computational search for biological sequences related to a query sequence. Alignment scores help identify candidate relatives in sequence databases.
Local alignment: An alignment that matches only the most similar subsections of sequences. It suits sequences sharing a conserved region but differing elsewhere.
Needleman–Wunsch algorithm: A dynamic-programming algorithm that finds an optimal global alignment between two sequences. It computes the best end-to-end match under a chosen scoring scheme.
Protein: A molecule made of amino-acid chains that performs structural, catalytic, and regulatory roles. Protein sequences are aligned to detect conserved residues and evolutionary relationships.

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