Glossary

Affine gap penalty

An affine gap penalty is assigned to gaps in an alignment (i.e., indels). In such a penalty, a gap of length L is penalized by a+b(L1), where a and b are constants chosen in advance. These constants represent, the gap opening penalty (a), which is charged for initiating the gap with its first symbol, and the gap extension penalty (b), which is charged for each subsequent symbol added to the gap.

The affine gap penalty is analogous to paying a cable bill in which you need to pay a one-time installation fee (a) and get the first month of TV free, followed by paying by a monthly charge (b).

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