Multiple alignment: An alignment of three or more sequences, with gaps inserted in the sequences such that residues with common structural position and/or ancestral residues are aligned in the same column of a multiple alignment.

Messenger RNA (mRNA): The complementary RNA copy of DNA formed from a single-stranded DNA template during transcription that migrates from the nucleus to the cytoplasm where it is processed into a sequence carrying the information to code for a polypeptide domain.

Motif: A conserved element of a protein sequence alignment that usually correlates with a particular function. Motifs are generated from a local multiple protein sequence alignment corresponding to a region whose function or structure is known. It is sufficient that it is conserved, and is hence likely to be predictive of any subsequent occurrence of such a structural/functional region in any other novel protein sequence.

Mutation: An inheritable alteration to the genome that includes genetic (point or single base) changes, or larger scale alterations such as chromosomal deletions or rearrangements.

Machine language: The set of commands that a computer's processor uses to carry out functions.

Match: In sequence alignment, the existence of the same base in a homologous position in both sequences.

Mismatch: A position in a double-stranded DNA molecule where base-pairing does not occur because the nucleotides are not complementary.

Molecular evolution: The gradual changes that occur in genomes over time due to the accumulation of mutations and structural rearrangements resulting from recombination and transposition.