Extension of EuGène's graph by a PCS to incorporate a single alternative transcript alignment. From the main graph (bottom) described in Figure 3, a Parallel Graph Subunit (PGS) is built (above) by duplicating the whole graph section involved in the EST alignment (between the graphs). Gene structure evidences provided by the alignment are taken into account in the PGS by forbidding the intergenic track all along the alignment, intronic tracks at match positions (light grey), and exonic tracks in gap positions (dark grey). Dotted arrows represent the two algorithm scans, the forward version from left to right, and the backward version from right to left. At the junction point in the PGS, an optimal prediction is obtained. Figure not to scale.