Gap opening and gap extension penalties


BLAST
program		 Default Gap
Penalty (G)		 Default Gap
Extension Penalty (E)		 Other supported (G)
and (E) values
blastp -11 -1 -10, -1;

-10, -2;

-11, -1;

-8, -2;

-9, -2
blastn -5 -2 none


Gap Costs. Gap costs for blastp and blastn are listed. The default penalty for opening a gap in blastp is -11; while the penalty for extending the gap is -1 (multiplied by the number of residues covered by the gap). Gap costs are an inherent part of the scoring system. Hence the selection of a substitution matrix other than the default in a BLAST 2.0 search also involves selecting an appropriate set of gap costs. Since insertion and mutation events are rare, but when they do occur, adjacent residues are often involved, the gap opening cost (G) is set relatively high (-10 - -15) and the gap extension cost (E) is set relatively low (-1 - -2).