**1.2 Analyzing retrofitted/ end-deleted BACs**

BACs deleted from an end, or inserted with exogenous DNA cassettes at the newly created ends of genomic inserts, are analyzed by isolating their DNA and separating them by Field Inversion Gel Electrophoresis (FIGE). The DNA in BAC clones is easily isolated by simple mini-prep procedures, digested with Not I enzyme and analyzed on FIGE (13, 25), as shown in Figure 3. High throughput formats for preparing DNA from BAC deletion clones in 96 well chambers, suitable for subsequent FIGE analyses and end sequencing, have also been described earlier (13, 25).

Fig. 3. Legend: FIGE display of an array of BAC deletion clone DNAs. DNA was isolated by the miniprep procedure from clones of a library of end-deleted BACs generated using a loxP transposon. The DNA was digested with Not I enzyme before electrophoresis. Lane 1 shows a 5 kb ladder, and lane 2 shows the DNA from the starting BAC clone.
