Figure 6

Implementation example with vertex sweep. An illustration of the first iteration of our algorithmic approaches for BSSI_{Λ, σ}: a) The cartoon representation of circularly permuted proteins S _a and S _b ; b) The problem represented as a graph where each node χ _i ∈ Λ represents an aligned fragment pair and each edge represents two inconsistent pairs; c) An illustration how sweep lines (dashed) can identify inconsistent aligned pairs as required to generate the interval clique inequalities. A rectangle is an ordered fragment pair (e.g., the solid green rectangle is the pair χ₅ = (${\lambda }_{5,3}^a,{\lambda }_{1,3}^b$)).