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Method, apparatus and computer program product for determining a set of non-hybridizing oligonucleotides

  • US 6,138,077 A
  • Filed: 06/03/1998
  • Issued: 10/24/2000
  • Est. Priority Date: 10/13/1994
  • Status: Expired due to Term
First Claim
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1. A computer program product comprising:

  • a computer usable storage medium having computer readable code embodied therein for causing a computer to generate a set of non-hybridizing oligonucleotides of a given length, said computer readable code comprising;

    computer readable program code configured to cause said computer to effect an assignment mechanism configured to assign a plurality of identifying data values representing different nucleotides;

    computer readable program code configured to cause said computer to effect a sequence generation mechanism configured to provide in a memory, from said plurality of identifying data values, a data-value sequence in a first set of possible sequences, where each possible sequence in said first set of possible sequences represents an oligonucleotide having a specified nucleotide at a specified residue position in said oligonucleotide of said given length;

    computer readable program code configured to cause said computer to effect a sequence comparison mechanism configured to compare in said memory said data-value sequence from said first set of possible sequences with a data-value sequence in a second set of possible sequences, on the basis of number of positions at which said data-value sequence from said first set of possible sequences and said data-value sequence in said second set of possible sequences have different data values;

    computer readable program code configured to cause said computer to effect a sequence inclusion mechanism configured to add said data-value sequence from said first set of possible sequences to said second set of possible sequences if the sequence comparison mechanism determined that said data-value sequence from said first set of possible sequences and said data-value sequence in said second set of possible sequences differ by at least N positions, where N is a specified value greater than one;

    computer readable program code configured to cause said computer to effect a sequence pair comparison mechanism configured to compare each pair of data-value sequences in said second set of possible sequences on the basis of number of positions at which each data-value sequence in said pair of data-value sequences have different data values;

    computer readable program code configured to cause said computer to effect a sequence retention mechanism configured to retain in said second set of possible sequences, data-value sequences that differ by said at least N positions from all other data-value sequences in said second set of possible sequences; and

    computer readable program code configured to cause said computer to effect a first iterative mechanism configured to repetitively invoke the sequence generation mechanism, the sequence comparison mechanism, the sequence inclusion mechanism, the sequence pair comparison mechanism and the sequence retention mechanism until a desired number of data-value sequences have been retained within said second set of possible sequences.

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