On the Analysis of Optical Mapping Data - University of Wisconsin ...

Figure 3.10 Schematic representation of“thinning”in optical map alignments. The horizontal
axis represents the underlying genome, with vertical lines indicating restriction sites. On
the left, optical maps are represented as intervals, while on the right they are viewed as
point events represented by the midpoint of the optical maps. The top panel in both plots
represent the true shotgun random sample of optical maps that originated from this region.
Actual optical maps obtained by image processing will have noise, including sizing errors,
missing cuts and false cuts, so not all these maps will be successfully aligned. Further, the
chance of being aligned may depend on the location of the map; for example, maps with
fewer fragments (from regions with fewer recognition sites) may be less likely to align than
maps of similar length with more fragments. In the bottom panels, which represent the
results of alignment, unaligned maps are indicated in grey. We ignore any possible errors
in the alignment step, assuming that they would be mild. Since the probability of being
successfully aligned depends on the origin, the locations of aligned maps, which is what we
actually observe, are no longer uniformly distributed.
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