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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 Οƒ = {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: βˆ’ a t βˆ’ g c c t a βˆ’ c g c a here the "βˆ’" indicates a "gap." the characters of each string must appear in order, and each column must contain a character from at least one of the strings. the score of an alignment is specified by a scoring matrix Ξ΄ of size (|Οƒ| + 1) Γ— (|Οƒ| + 1), where the extra row and column are to accommodate gaps. for instance the preceding alignment has the following score: Ξ΄(βˆ’, t) + Ξ΄(a, a) + Ξ΄(t, βˆ’) + Ξ΄(βˆ’, c) + Ξ΄(g, g) + Ξ΄(c, c) + Ξ΄(c, a). give a dynamic programming algorithm that takes as input two strings x[1 . . n] and y[1 . . m] and a scoring matrix Ξ΄, and returns the highest-scoring alignment. the running time should be o(mn).

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