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Minimization of surprisal data through application of hierarchy filter pattern

  • US 10,353,869 B2
  • Filed: 06/08/2012
  • Issued: 07/16/2019
  • Est. Priority Date: 05/18/2012
  • Status: Active Grant
First Claim
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1. A method of minimizing surprisal data representing an entire genome of an organism for compression and transmission, comprising a source computer having one or more processors and one or more computer-readable memories coupled to the one or more processors performing the steps of:

  • a) reading and identifying characteristics of the organism'"'"'s medical history and background associated with a genetic sequence of an organism;

    b) receiving an input of rank of at least two identified characteristics associated with the genetic sequence of the organism;

    c) generating a hierarchy of ranked, identified characteristics based on the rank of the at least two identified characteristics associated with the genetic sequence of the organism;

    d) comparing the hierarchy of ranked, identified characteristics to a repository of reference genomes; and

    e) if at least one reference genome from the repository matches the hierarchy of ranked, identified characteristics,i) storing the at least one matched reference genome in a repository;

    ii) breaking the at least one matched reference genome into pieces comprising nucleotides of the genetic sequence which comprises at least one gene, at least some of the pieces being associated with the identified characteristics;

    iii) storing the pieces which are associated with the identified characteristics in the repository;

    iv) combining the stored pieces of the at least one matched reference genome into a filter pattern;

    v) comparing pieces of the nucleotides of the genetic sequence of the organism which comprises at least one gene which correspond to the stored pieces of the at least one matched reference genome to the nucleotides of the filter pattern of the pieces of the at least one matched reference genome, to find differences where nucleotides of the genetic sequence of the organism which are different from the nucleotides of the at least one matched reference genome;

    vi) using the differences to create surprisal data representing an entire genome of the organism and storing the surprisal data in the repository, the surprisal data comprising a starting location of the differences within the reference genome, how the reference genomes were broken into pieces, a count of a number of differences at the location within the at least one matched reference genome and the nucleotides from the genetic sequence of the organism which are different from the nucleotides of the reference genome; and

    vii) transmitting to a destination, a compressed, minimized genome representing an entire genome by sending the surprisal data, an indication of the at least one matched reference genome, and how the reference genome were broken into pieces, and not sending sequences of nucleotides that are the same in the genetic sequence of the organism and the at least one matched reference genome.

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