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

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Chapter 3
Significance of Optical Map Alignments
3.1 Introduction
Physical maps describe the locations of one or more markers on a genome and can be
viewed as a coarse summary of the full DNA sequence. Restriction maps are physical maps
induced by restriction enzymes, naturally produced by bacteria to defend themselves by
cutting up (or restricting) foreign DNA. The marker associated with a restriction enzyme
is a specific pattern it recognizes and cleaves; typically a palindromic DNA sequence 4 to 8
base pairs long. Optical mapping (Schwartz et al., 1993; Dimalanta et al., 2004) is a single
molecule approach for the construction of ordered restriction maps of genomic DNA. DNA
molecules broken apart using a shotgun process are stretched and attached to a positively
charged glass support. When a restriction enzyme is applied, it cleaves the DNA at sites
recognized by the enzyme. The DNA molecules remain attached to the surface, but the
elasticity of the stretched DNA pulls back the molecule ends at the cleaved sites. After
being stained with a fluorochrome, these sites can be identified under a microscope as tiny
gaps in the fluorescent line of the molecule, giving a local snapshot of the full restriction
map.
Noise: Unlike other restriction mapping techniques, optical mapping bypasses the problem
of reconstructing the order of the restriction fragments. However, optical map data are not
perfect: the inter-site fragment sizes are not measured exactly, some true recognition sites
may go undigested by the enzyme or unidentified by image processing, some spurious cuts