The above scheme showed a simple length-dependent weighting for gaps.
Thus two isolated gaps give the same score as two consecutive gaps. It
is possible to generalise the algorithm to allow gaps of length greater
than 1 to carry weights other than the simple sum of single gap weights
[27]. Such gap weighting can give a more biologically
meaningful model of transitions from one sequence to another since
insertions and deletions of more than one residue are not uncommon
events between homologous protein sequences. Most computer programs
that implement dynamic programming allow gaps to be weighted with the
form where
is the gap length and
and
are constants
, since this can be computed efficiently [28].