forms of γ( ane gap score, in which the s gaps regardless of length, and a γ(g) = −d − (g − 1)e. is can b S(so...i , I(so...i , Speciﬁc gap penalty function: e gap penalties n specic forms of γ(g) the computation can be bounded. e common case score, in which the score of a gap depends on only two values, an initiation dless of length, and an extension cost e for each additional base in the gap. In − (g − 1)e. is can be computed by the following recurrences: S(so...i , t0...j ) = max σ(si , tj ) + S(s0...i−1 , t0...j−1 ) σ(si , tj ) + I(s0...i−1 , t0...j−1 ) I(so...i , t0...j ) = max −d + S(s0...i , t0...j−1 ) −e + I(s0...i , t0...j−1 ) −d + S(s0...i−1 , t0...j ) −e + I(s0...i−1 , t0...j )