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Oligonucleotide probes for genosensor chips

  • US 20040111221A1
  • Filed: 04/09/2003
  • Published: 06/10/2004
  • Est. Priority Date: 04/09/2002
  • Status: Active Grant
First Claim
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1. A software system for designing and selecting oligonucleotide probes for use in DNA microarray, said software system comprising program instructions for:

  • (a) inputing target DNA sequences;

    (b) creating an internal DNA database table that includes the entire target DNA sequences from which oligonucleotide probes are selected;

    (c) generating a primary table of oligonucleotides that contains all possible probes of a defined length that can be derived from said DNA target sequences;

    (d) creating a secondary table of probes that only contains probes with appropriate composition and thermodynamic properties according to user-defined selection criteria;

    (e) selecting from said secondary table specific probes based on methods that evaluate similarity between the probes in said secondary table and selected targeted DNA molecules; and

    (f) performing virtual hybridization to analyze possible hybridization of said oligonucleotide probes against the DNA sequences in said internal DNA database, wherein said analysis shows target sites for perfect hybridization as well as sites that could be potential sites for ambiguous hybridization.

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