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Method of identifying virtual representations of nucleotide sequences

  • US 8,694,263 B2
  • Filed: 05/21/2004
  • Issued: 04/08/2014
  • Est. Priority Date: 05/23/2003
  • Status: Active Grant
First Claim
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1. 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≧



    108;

    (ii) 300≧

    K≧

    30;

    (iii) the integer closest to (log4(Z)+2)≧

    L1

    the integer closest to log4(Z);

    (iv) X is the integer closest to D1×

    (K−

    L1+1);

    (v) Y is the integer closest to D2×

    (K−

    L1+1);

    (vi) 1.5≧

    D1

    1; and

    (vii) 1>

    D2

    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 L1-mers occurring in each oligonucleotide; and

    (F) selecting one or more oligonucleotides that have a sum total value of L1-mer counts in the virtual representation of no fewer than Y and no more than X, wherein an L1-mer is a subregion of the oligonucleotide having a length of L1 nucleotides, wherein an L1-mer count is the number of times the sequence represented by one L1-mer occurs in the genome, and wherein the sum total value of L1-mer counts is the sum of every L1-mer count of the oligonucleotide occurring in the virtual representation.

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