Patent ID: 8481699

Claim:
An isolated barcoded Paired-End Ditag (bPED) nucleic acid fragment, comprising: (a) a barcoded adaptor, comprising: (i) a barcode, comprising at least one base pair of a known nucleotide sequence; (ii) a 5′-flanking sequence, comprising a first restriction enzyme (RE) recognition site; and (iii) a 3-flanking sequence, comprising a second RE recognition site and covalently linked to the 5′-flanking sequence via the barcode; wherein the length of the barcoded adaptor is 18 or fewer base pairs, and the first and the second REs are the same or different and they each allow binding of specific restriction enzymes that lead to cleavage of a nucleic acid sequence at a defined distance from their respective recognition sites; (b) a first tag; and (c) a second tag, covalently linked to the first tag via the barcoded adaptor; wherein the first tag corresponds to the 5′-end of a nucleic acid molecule, and the second tag corresponds to the 3′-end of the nucleic acid molecule, and the sequence of the nucleic acid molecule is unknown.