Patent ID: 8694263

Claim:
A method of identifying an oligonucleotide, the method comprising (A) cleaving a genome of at least Z basepairs in silico with a restriction enzyme to generate a plurality of predicted nucleic acid molecules, (B) generating a virtual representation of said genome by identifying predicted nucleic acid molecules, wherein each predicted nucleic acid molecule has a length of 200-1,200 basepairs, inclusive; (C) calculating the following: (i) Z≧1×10 8 ; (ii) 300≧K≧30; (iii) the integer closest to (log 4 (Z)+2)≧L 1 ≧the integer closest to log 4 (Z); (iv) X is the integer closest to D 1 ×(K−L 1 +1); (v) Y is the integer closest to D 2 ×(K−L 1 +1); (vi) 1.5≧D 1 ≧1; and (vii) 1>D 2 ≧0.5; (D) selecting oligonucleotides each having a length of K nucleotides, inclusive, and each with at least 90% sequence identity to a predicted nucleic acid molecule in (B); (E) identifying all of the L 1 -mers occurring in each oligonucleotide; and (F) selecting one or more oligonucleotides that have a sum total value of L 1 -mer counts in the virtual representation of no fewer than Y and no more than X, wherein an L 1 -mer is a subregion of the oligonucleotide having a length of L 1 nucleotides, wherein an L 1 -mer count is the number of times the sequence represented by one L 1 -mer occurs in the genome, and wherein the sum total value of L 1 -mer counts is the sum of every L 1 -mer count of the oligonucleotide occurring in the virtual representation.