Fig. 1

Example of a genomic map and strategies for glocal and overlap map alignment. a Example of an experimental or in silico map with ordered fragment sizes. bFeasible match within dashed bars (Definition 1). cComposite seeds with c=2 (Definition 4), where Composite (iv) represents the final composition of seeds with errors used here; the case with one false cut allowed is not directly indexed from the in silico maps, but is explored during the seed search process. d Seed extension in glocal alignment with dynamic programming (straight lines delimit feasible matches found, dashed lines mark truncated end matches and dashed circles show potentially missing fragments). e Sliding-window approach in overlap alignment: for a particular window of fixed size (dashed black border) we first compute a glocal alignment (solid yellow border) from one of its seeds (multicolored box), statistically evaluate it and subsequently extend it until the end of one of the maps is reached on both sides of the seed