Schematic representation of EMERALD's safety window calculation of a DIAMOND DeepClust cluster containing 4 member sequences. EMERALD performs a pairwise global alignment between the cluster representative against each of the 4 cluster member sequences using affine gap costs and BLOSUM62 as substitution matrix. For the first sequence pair, the right-hand side illustrates the suboptimal alignment graph and their corresponding suboptimal alignment configurations between the two sequences listed as - suboptimal alignments (an alignment is - suboptimal if its score is not more than smaller than the optimal score). The illustrated graph is one of minimum size to fulfill the property of including all -suboptimal alignments (here, we choose = 8 ). Source-to-sink paths in the graph correspond to suboptimal alignments; nodes and edges on the unique optimal alignment path are shown in black, while those configurations on a -suboptimal path are illustrated in gray. The optimal alignment path is color coded in black and the two top - suboptimal alignment paths illustrated in orange and blue. For = 0.75 and = 8 , we obtain three safety windows shown as green intervals. These three colored safety windows correspond to subpaths contained in at least =0.75 (i.e., 75% ) of all source-to-sink paths (i.e., of all -suboptimal alignments). Note that the middle safety window is not captured (i.e., contained) by the (unique) optimal alignment, in black, and is only revealed by the subgraph of all -suboptimal alignments. Finally, we project the safety windows onto the cluster member (and cluster representative sequence) as explained in (the Methods " section). This procedure is repeated for all possible pairwise comparisons between the representative sequence and the 4 members, thereby obtaining (, ) -safety windows for each cluster member (bottom left)
