Patent ID: 8178300

Claim:
A method for identifying the clonal source of a restriction fragment, comprising: (a) providing a sample DNA; (b) generating an artificial chromosome clone bank wherein each artificial chromosome clone contains part of the sample DNA; (c) combining the artificial chromosome clones in a plurality of pools, wherein each clone is present in more than one pool, to create a library; (d) digesting the artificial chromosome clones in the plurality of pools with one or more restriction endonucleases to provide for a set of restriction fragments for each pool; (e) ligating adaptors to one or both sides of the restriction fragments, wherein at least one adaptor contains a pool-specific identifier or a degenerate identifier section, respectively, to provide adaptor-ligated restriction fragments; (f) sequencing at least the pool-specific identifier and part of the restriction fragment; and (g) assigning the restriction fragment sequences of step (f) to the corresponding clones using the pool-specific identifiers, wherein a pool-specific identifier identifies the clonal source of a restriction fragment.