An example where greedy extraction of gap-restricted co-linear chains may result into more pieces than optimal. Greedy selection would align blocks 2, 3, 4 with dashed edges, but then with suitable gap-restriction blocks 1 and 5 could not be aligned together, and the assembly would be split into 3 parts. Optimal algorithm can choose 2 and 4 with dashed edges and then blocks 1, 3, 5 together, resulting into 2 parts only. It is possible to construct such an example even without multiple mappings for the blocks.
Mäkinen et al. BMC Bioinformatics 2012 13:255 doi:10.1186/1471-2105-13-255