Fig. 9

Principle of the Gap Insertion algorithm. Image illustrates the state when in proteins a and b the helices i and r were already determined as the corresponding ones and the pointers (red arrows) are positioned behind them. Now the strand j from a is searched in b and the corresponding strand t is found after skipping one secondary structure (thick line). Therefore n _gap =1. Similarly, for helix s in B we search for corresponding helix in A. It is the m helix in A (thick line) and we had to skip 3 secondary structures, so m _gap =3. So we select the first option as the next step, insert one gap to chain a (which will correspond to helix s from b), shift the pointers behind j, respectively t, and repeat the procedure until both proteins are processed