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Method for identifying suitable nucleic acid probe sequences for use in nucleic acid arrays

  • US 7,894,998 B2
  • Filed: 06/26/2002
  • Issued: 02/22/2011
  • Est. Priority Date: 06/26/2002
  • Status: Active Grant
First Claim
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1. A method of identifying candidate probe sequences for a nucleic acid sequence for use as probes in a nucleic acid array, said method comprising:

  • (a) providing a set of known, undesirable probe sequences present in a format representative of the nucleotide sequences of said known, undesirable probe sequences, wherein said set of undesirable probe sequences comprises probe sequences that do not meet a predetermined specificity of binding affinity for said nucleic acid sequence;

    (b) comparing said nucleic acid sequence present in a format representative of the nucleotide sequence of said nucleic acid sequence to each member of said set;

    (c) marking regions of said nucleic acid sequence that have no more than 5 mismatches with a sequence of a member of said set as undesirable regions for candidate probe sequences for said nucleic acid sequence;

    (d) identifying candidate probe sequences for said nucleic acid sequence for use as probes in a nucleic acid array from unmarked regions of said nucleic acid sequence; and

    (e) synthesizing at least one of said identified candidate probe sequences.

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