Figure 1

Probe design from the shortest path on a graph. The de Bruijn graph for all possible DNA base doublets and one possible solution for a shortest path represented as a pseudo-Eulerian cycle (bold edges). The reverse complement solution is represented by dashed edges in the graph and also the inner cycle sequence. "Cutting" the circular sequence while retaining one overlapping base results in two sequences of total length 12 (containing all doublets) as compared to the length of all non-overlapping concatenated doublets 2 * 4² = 32. Cutting the circular sequence at different points allows screening multiple replicates and helps identify biases in sequence recognition preferences. Reverse complement strands for the replicates are not shown.