Estimating the fraction of clonable genomic DNA

Tang and Waterman (1990, Bulletin of Mathematical Biology, 52, 455-475) give an estimate of the fraction of clonable genomic DNA by complete digestion with a single restriction enzyme. However, their argument neglects the 'end effects' of restriction enzyme digestion. This effectively assumes that the DNA is of infinite length. However, neglecting the end effects is not necessary to obtain useful estimates of the fraction of clonable DNA. An alternative approach is taken to estimating the fraction of clonable DNA that accounts for the finite nature of the DNA strand. This approach yields the Tang and Waterman estimate by allowing the genome length to go to infinity. Comparisons based on simulation studies show the finite approach to be more accurate than Tang and Waterman's estimate, especially for shorter genomes. Sequence-based studies also show that the proposed method is often superior to the Tang-Waterman estimate.