Figure 5: Directed graph analysis approach used in ThermoAlign to identify primer pairs for an amplicon tiling path at a targeted region.
From: ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing
xi and yi represent forward and reverse primers respectively. Nodes correspond to expected amplicons (depicted as colored bars), which are ordered by their base pair coordinates. Directed edges (lines with an arrowhead) are drawn between overlapping amplicons, which in this case forms two subgraphs. Edge weights (depicted by the thickness of the lines representing edges; here, thicker lines represent the smaller weighted edges that would be selected) are computed based on the cumulative coverage and amount of overlap. Dijktra’s shortest path algorithm is applied to each subgraph to identify the primer pairs comprising the minimum tiling path of amplicons (black colored edges). As portrayed by the blue and yellow coloring, two groups of non-overlapping primer pairs are designated for multiplex consideration. The expected coverage for this example minimum tiling path is indicated by black (covered) and white (gaps) fill.
