How to detect similarity of genes?
DNA and protein molecules evolve mostly by three
processes: point mutations (exchange of a single letter for
another), insertions, and deletions. If two genes have
evolved from a common ancestral gene, then it should be
possible to detect the similarity by inserting gaps into the
two sequences that correspond to insertions and deletions
so that the nucleotides derived from common ancestral
nucleotides end up on top of each other. This process is
known as sequence alignment. The columns of the
alignment should show significantly more nucleotide
identities than would be expected by chance.