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Methods for evaluating oligonucleotide probes of variable length

  • US 20040009484A1
  • Filed: 07/11/2002
  • Published: 01/15/2004
  • Est. Priority Date: 07/11/2002
  • Status: Abandoned Application
First Claim
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1. A method for predicting the potential of a hybridization oligonucleotide of length greater than about 20 nucleotides to hybridize to a target nucleotide sequence, said method comprising:

  • (a) identifying a predetermined number of unique oligonucleotides of at least about 20 nucleotides in length within a nucleotide sequence of at least about 30 nucleotides in length that is hybridizable with said target nucleotide sequence, said oligonucleotides being chosen to sample a length of said nucleotide sequence, (b) determining and evaluating for said oligonucleotides at least one parameter that is predictive of the ability of said oligonucleotides to hybridize to said target nucleotide sequence, (c) selecting a subset of oligonucleotides within said predetermined number of unique oligonucleotides based on an examination of said parameter and application of a rule that rejects some of said oligonucleotides of step (b), (d) identifying oligonucleotides in said selected subset, viewed according to order of position along said nucleotide sequence, that are in clusters along a region of said nucleotide sequence and that identify a contig in said nucleotide sequence, (e) selecting for a cluster a hybridization oligonucleotide that comprises at least a portion of the nucleotide sequence of said contig wherein said hybridization oligonucleotide is different from any of the oligonucleotides in (d) which identify the contig.

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