When a new gene is discovered, a standard approach to understanding its function is to look through a database of known genes and find close matches. the closeness of two genes is measured by the extent to which they are aligned. to formalize this, think of a gene as being a long string over an alphabet σ = {a, c,g, t}. consider two genes (strings) x = atgcc and y = tacgca. an alignment of x and y is a way of matching up these two strings by writing them in columns, for instance: