Fig. 4
From: HH-suite3 for fast remote homology detection and deep protein annotation
Two approaches to reduce the memory requirement for the DP score matrices from O(LqLt) to O(Lt), where Lq and Lt are lengths of the query and target profile, respectively. (Top) One vector holds the scores of the previous row, SXY(i−1,·), for pair state XY ∈{MM, MI, IM, GD and DG}, and the other holds the scores of the current row, SXY(i,·) for pair state XY ∈{MM, MI, IM, GD and DG}. Vector pointers are swapped after each row has been processed. (Bottom) A single vector per pair state XY holds the scores of the current row up to j−1 and of the previous row for j to Lt. The second approach is somewhat faster and was chosen for HH-suite3