Figure 1
From: Optimizing substitution matrix choice and gap parameters for sequence alignment
A typical Q function. The graphs show alignment accuracy (vertical axis) on all pairs in BALIBASE v2 as a function of extension penalty e (horizontal axis) with fixed gap-open penalty g = 6.5 and the BLOSUM70 matrix. The interval outlined in the dashed box on the left is expanded on the right. Note the many local maxima, and that trends are apparent with changes in Q of around 0.01 (left), while smaller changes are typically "noise". (right).