Fig. 3.

Schematic representation of the search tree structure. Note that we use here a ‘sequence as edge’ representation, which allows displaying the length of individual sequences in a convenient way. In this representation, the length of each edge is proportional to the corresponding sequence length. The black edges define P, the path determined so far. The dotted edges are the ones that correspond to candidates that were rejected during previous iterations. The tree T rooted at p_|P| is displayed with gray edges. T is increased by steps as represented by the four numbered dotted arcs. The program examines the paired-end matches between T and individual segments in P. This structure allows connecting paired end issued from inserts that are as long as the length of P