Patent ID: 7662559

Claim:
A method of determining a relative location of a target nucleotide sequence on a polynucleotide, the method comprising: obtaining an ordered map of the polynucleotide according to a method comprising: fragmenting the polynucleotide to generate a library of polynucleotide fragments; identifying sequences in each of the polynucleotide fragments in the library, by a method comprising: (a) cleaving the polynucleotide sequence with a first type-IIs endonuclease; (b) ligating a first adapter sequence to the polynucleotide sequence cleaved in step (a), said first adapter having a recognition site for a second type-IIs endonuclease, the recognition site being oriented so that the second type-IIs endonuclease has a cleavage site in the polynucleotide sequence; (c) cleaving the polynucleotide sequence resulting from step (b), with the second type-IIs endonuclease; (d) ligating a second adapter sequence to the polynucleotide sequence cleaved in step (c); and determining the sequence of nucleotides of the polynucleotide sequence between the first and second adapter sequences; comparing the sequences identified in each fragment with the sequences identified in each other fragment to obtain a level of correlation between each fragment and each other fragment; and ordering the fragments according to their level of correlation to generate an ordered map of the polynucleotide; (ii) fragmenting the polynucleotide; (iii) determining which fragment generated in step (ii) includes the target nucleotide sequence; and (iv) correlating a marker on the fragment identified in step (iii) with a marker on the ordered map to identify the approximate location of the target nucleotide sequence on the polynucleotide.