The schematic illustration of FATCAT structural alignment by chaining AFPs in a constrained alignment region defined by TOPS alignment output. (a) In FATCAT, two fragments form an AFP (shown as a line in the graph) according to the criteria (see text). (b) The alignment of secondary structure elements from TOPS+ comparison is used to define the constrained area for AFP detection, in which each two aligned secondary structure elements defines an "eligible" block (shown as filled squares). These blocks may be disconnected, and we need to connect them with connecting blocks (shown as open squares). (c) We add a buffer area surrounding the constrained area defined in (b) (shown as the area closed by dashed lines) to get the constrained alignment region for FATCAT alignment (show as the area closed by dark lines). (d) Only those AFPs within the constrained alignment region are used in the dynamic programming algorithm for chaining.