Key background concept: physical mapping

A physical map consists of a set of identifiable landmarks along the chromosome. Physical distance is measured in base pairs. The physical map differs from the genetic map, which is based on genetic linkage data.

Physical maps are commonly constructed from BAC libraries, by identifying sets of overlapping clones, and them arranging them into a linear order (called a "contig")‏

An example of a small part of the physical map of Arabidopsis, taken from TAIR, http://www.arabidopsis.org/)