Aﬃne gap penalties

. Ane gap penalties

For certain specic 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

)