Chaining of Matching Fragment Pairs. A schematic representation of MFPs for two proteins with sequences S1 and S2. MFPs are indicated as pairs of rectangles connected by a line mapped onto the sequence in panel (a) and as nodes of a graph in corresponding colors in (b). The graph representation encodes the topological relations between the MFPs. E.g. F3 can be chained with F6 but it cannot be chained with F5, because F5 involves a fragment on sequence S1 that is upstream of the corresponding fragment of F3 on sequence S1 (Panel (a)). In the graph-representation, such a situation results in no edge assigned to the pair of vertices representing F3 and F5. By choosing an appropriate weight function for the edges (see text), the longest path corresponds to the best alignment between the two structures as represented here by thick red arrows.
Mosca et al. BMC Bioinformatics 2008 9:352 doi:10.1186/1471-2105-9-352