×

Design and selection of genetic targets for sequence resolved organism detection and identification

  • US 7,668,664 B2
  • Filed: 08/22/2007
  • Issued: 02/23/2010
  • Est. Priority Date: 07/02/2004
  • Status: Expired due to Fees
First Claim
Patent Images

1. A computer-implemented method comprising:

  • providing a list of target sequences associated with one or more organisms in a list of organisms;

    providing a list of candidate prototype sequences suspected of hybridizing to one or more of the target sequences;

    generating a collection of probes corresponding to each candidate prototype sequence, each collection of probes comprising a set of probes for every subsequence having a predetermined, fixed subsequence length of the corresponding candidate prototype sequence, the set consisting of the corresponding subsequence and every variation of the corresponding subsequence formed by varying a center nucleotide of the corresponding subsequence;

    generating a set of fragments corresponding to each target sequence, each set of fragments comprising every fragment having a predetermined, fixed fragment length of the corresponding target sequence;

    calculating the binding free energy of each fragment with a perfect complementary sequence of the fragment, and if any binding free energy is above a predetermined, fixed threshold, the fragment is extended one nucleotide at a time until the binding free energy is below the threshold or the fragment is the same length as the probes corresponding to the corresponding target sequence, generating a set of extended fragments; and

    determining which extended fragments are perfect matches to any of the probes; and

    assembling a base call sequence corresponding to each candidate prototype sequence comprising;

    a base call corresponding to the center nucleotide of each probe of the corresponding prototype sequence that is a perfect match to any extended fragment, but for which the other members of the set of probes containing the perfect match probe are not perfect matches to any extended fragment; and

    a non-base call in all other circumstances;

    wherein the method is at least partly performed using a suitably programmed computer.

View all claims
  • 1 Assignment
Timeline View
Assignment View
    ×
    ×