The example of difficult non-sequential alignment taken from MALISAM-ns set. (a) The structure of Formiminotransferase domain of formiminotransferase-cyclodeaminase (SCOP-ID d1qd1b1, B2083-B2180) and the permuted structure of FAD-binding domain (SCOP-ID d1n62c2, C1-C61). (b) The alignment plot of the reference alignment. The horizontal axis and the vertical axis correspond to residue positions of d1qd1b1 and those of permuted d1n62c2, respectively. Positions of α -helices and β -strands in the native structure are also indicated by red and blue bars. (c) Comparison of the agreement between the reference alignment and nine alignment methods we tested here. The name of method and its Q-score for the protein pair is shown on each the alignment plot. The reference alignment pairs are shown in black circles. Alignment pairs generated by each methods are shown in red circles.