Efficacy of clone fingerprinting methodologies

With the development of new high-information content fingerprinting techniques for constructing BAC-based physical maps, physical map construction is accelerating and it is important to determine which methodologies work best. In a recent publication (Z. Xu et al., 2004, Genomics 84:941-951), Xu et al. evaluated five different techniques (one agarose-based and four using multiple enzymes) and concluded that a two-enzyme technique was superior. In addition, they found that no benefit was gained from fingerprinting more than 10x coverage. In this paper we report our own extensive simulation results, which lead to contrasting conclusions. Our data indicate that the five-enzyme method known as SNaPshot is the most effective and that the assembly can in fact be significantly improved with greater than 10x coverage.