Figure 8.

The Collapse module consensus assignments. Boxes, shown in white, represent consensus regions on the ‘Gene’, and the ‘New assignment’ boxes, in black, represent the possible outcomes of collapsing the initial assignments. The Collapse module seeks to allow cases A and B without allowing case C (Chaining). In case A, the two regions from the same homologous superfamily overlap to a great enough extent that they are merged together. In case B, one region is contained within another region of the same homologous superfamily and they are merged. In case C, it is clear that the top and bottom regions do not overlap, so merging of all four regions is not allowed.