Gap penalty

A gap penalty is the score cost of introducing an insertion or deletion into a sequence alignment.

An affine gap penalty charges $o$ for the first position of a gap and $e$ for each additional position. With $o>e$, one long gap costs less than several separate gaps of the same total length. Some software instead uses $o+e\ell$; numerical settings must be interpreted with their convention.

A linear gap penalty assigns a cost proportional to gap length: $g(\ell )=e\ell$ for $e>0$. One gap of length three and three gaps of length one therefore incur the same total cost, before considering alignment substitutions. An affine gap penalty distinguishes opening from extending a gap and can favour fewer longer gaps. The chosen cost is part of the alignment model rather than an experimentally measured universal price of an insertion. ^[ref]