WholeGenome Physical Mapping: An Overview on Methods for DNA Fingerprinting
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abstract
DNA fingerprinting combined with the technologies of large DNA fragment cloning in bacteria has become the most widely used approach to whole-genome physicalmapping with large-insert clones. To facilitate effective use of this approach for whole-genome physical mapping, this chapter provides an overview of the major fingerprinting methods developed to date, including the agarose gel-based restriction fingerprinting method, the manual sequencing or polyacrylamide gelbased restriction fingerprinting method, and the automatic sequencing gel-and capillary electrophoresis-based restriction fingerprinting method. The procedures of the fingerprinting methods that have been used or that have potential for wider utilization are detailed. Analysis of the whole-genome physical maps developed to date by using the fingerprinting methods and the most recent comparative studies among different fingerprinting methods have shown that quality contig map construction is significantly affected by fingerprinting methods. A capillary electrophoresis-based, two-or three-enzyme fingerprinting method seems to be the most efficient for whole-genome physical mapping, although any of the fingerprinting methods could be used to generate fingerprints and to construct contig maps from large-insert clones. It is also observed from these studies that other tools such as DNA markers of genetic maps are needed to assist in the construction of robust physical maps consisting of one or a few contigs for each chromosome from the fingerprints of the source clones generated by the fingerprinting methods. New techniques or strategies are also needed to construct contig maps for the genomic regions that are abundant in tandem repeats such as centromeric and rDNA repeats. 2005 WILEY-VCH Verlag GmbH and Co.
