Network formulation

The spliced alignment problem can be formulated in network terms. The set of blocks $\mathcal{B}= \{B_i\}_{i=1}^{L}$ is represented by a set of nodes $\{v_i\}_{i=1}^{L}$. A node v_i is connected to a node v_j if B_i < B_j. The requested solution is the best alignment between the reference sequence (T) and a path in the network.