Alu-PCR Fingerprinting of YACs

Random fingerprinting strategies have been applied to a number of genome projects using unordered collections of phage or cosmid clones, e.g., Escherichia coli (1 ), Saccharomyces cerevisiae (2 ), and Caenorhabditis elegans (3 ). Overlaps were identified between either phage or cosmid clones using a fingerprinting method based on restriction endonuclease digestion. In each case the success of the method depended on the ability to generate and resolve sufficient numbers of bands in each fingerprint to detect as many as possible of the potential overlaps. Yeast artificial chromosomes (YACs) are not amenable to the same methods because of the presence of the yeast genome DNA in equimolar or higher amounts and because it is not possible to purify the artificial chromosome as it has no physical properties to distinguish it from the host DNA.