1. A method of isolating fragment tags from genomic DNA, the method comprising: (a) shearing a preparation of genomic DNA to fragments about 3-5 kb in length; and (b) digesting the preparation of genomic DNA with a restriction enzyme; wherein (a) and (b) can occur in either order or concurrently and wherein (a) and (b) produce a collection of DNA fragments comprising at least some DNA fragments comprising a restriction site at one end and which are blunt at the other end; and (c) isolating DNA fragments about 1 kb in length from the collection of DNA fragments, which DNA fragments are the fragment tags.