Parallelization of surprisal data reduction and genome construction from genetic data for transmission, storage, and analysis

A method of recreating an entire genome of the organism from a reference genome and surprisal data using a computer having a plurality of computer processing elements, the surprisal data comprising a starting location of the differences within the reference genome, and the nucleotides from the genetic sequence of the organism which are different from the nucleotides of the reference genome, discarding sequences of nucleotides that are the same in the genetic sequence of the organism and the reference genome, the method comprising the steps of:

• the computer retrieving surprisal data from a repository and dividing the surprisal data into parts;
• the computer retrieving the reference genome from the repository and dividing the reference genome into parts corresponding to the parts of the surprisal data;
• the computer assigning parts of the reference genome and corresponding parts of the surprisal data to a plurality of computer processing elements;
• the computer within each computer processing element, altering the parts of the assigned reference genome based on the corresponding part of the surprisal data by replacing nucleotides at each location in the assigned parts of the reference genome specified by the corresponding parts of surprisal data with the nucleotides from the genetic sequence of the organism in the surprisal data associated with the location and storing the altered parts of the reference genome in the repository;
• and
• the computer retrieving the altered parts of the reference genome in the repository combining the altered parts of the reference genome together, resulting in an entire genome of the organism.

A computer program product for reducing an amount of data representing a genetic sequence of an organism using a computer having a plurality of computer processing elements, the computer program product comprising:

• one or more computer-readable, tangible storage devices;
• program instructions, stored on at least one of the one or more storage devices, to divide a reference genome and the genetic sequence of the organism into parts and assign each of the parts of the reference genome and the parts of the genetic sequence of the organism to one of the plurality of computer processing elements;
• within each computer processing element, program instructions, stored on at least one of the one or more storage devices, to compare the nucleotides of the assigned part of the genetic sequence of the organism to nucleotides of the assigned part of the reference genome, to find differences where nucleotides of the genetic sequence of the organism are different from the nucleotides of the assigned part of the reference genome, and store surprisal data in a repository, the surprisal data comprising at least a starting location of the differences within the assigned part of the reference genome, and the nucleotides from the genetic sequence of the organism which are different from the nucleotides of the assigned part of the reference genome, discarding sequences of nucleotides that are the same in the genetic sequence of the organism and the assigned part of the reference genome;
• program instructions, stored on at least one of the one or more storage devices, to retrieve the parts of the surprisal data from the repository;
• program instructions, stored on at least one of the one or more storage devices, to combine the parts of the surprisal data from the repository to form a complete set of surprisal data representing the differences between the genetic sequence of the organism and the reference genome;
• program instructions, stored on at least one of the one or more storage devices, to store the complete set of surprisal data in the repository;
• program instructions, stored on at least one of the one or more storage devices, to recreate an entire genome of the organism by:
• retrieving the surprisal data from the repository and dividing the surprisal data into parts;
• retrieving the reference genome from the repository and dividing the reference genome into parts corresponding to the parts of the surprisal data;
• assigning parts of the reference genome and corresponding parts of the surprisal data to each of a plurality of computer processing elements;
• within each computer processing element altering the parts of the assigned reference genome based on the corresponding part of the surprisal data, by replacing nucleotides at each location in the assigned parts of the reference genome specified by the corresponding parts of surprisal data with the nucleotides from the genetic sequence of the organism in the surprisal data associated with the location, and storing the altered parts of the reference genome in the repository;
• retrieving the altered parts of the reference genome from the repository;
• and
• combining the altered parts of the reference genome together, resulting in an entire genome of the organism.

A computer program product for recreating an entire genome of the organism from a reference genome and surprisal data using a computer having a plurality of computer processing elements, the surprisal data comprising a starting location of the differences within the reference genome, and the nucleotides from the genetic sequence of the organism which are different from the nucleotides of the reference genome, discarding sequences of nucleotides that are the same in the genetic sequence of the organism and the reference genome, the computer program product comprising:

• one or more computer-readable, tangible storage devices;
• program instructions, stored on at least one of the one or more storage devices, to retrieve surprisal data from a repository and dividing the surprisal data into parts;
• program instructions, stored on at least one of the one or more storage devices, to retrieve the reference genome from the repository and dividing the reference genome into parts corresponding to the parts of the surprisal data;
• program instructions, stored on at least one of the one or more storage devices, to assign parts of the reference genome and corresponding parts of the surprisal data to a plurality of computer processing elements;
• within each computer processing element, program instructions, stored on at least one of the one or more storage devices, to alter the parts of the assigned reference genome based on the corresponding part of the surprisal data by replacing nucleotides at each location in the assigned parts of the reference genome specified by the corresponding parts of surprisal data with the nucleotides from the genetic sequence of the organism in the surprisal data associated with the location and store the altered parts of the reference genome in the repository;
• and
• program instructions, stored on at least one of the one or more storage devices, to retrieve the altered parts of the reference genome in the repository combining the altered parts of the reference genome together, resulting in an entire genome of the organism.

A computer system for reducing an amount of data representing a genetic sequence of an organism, using a computer having a plurality of computer processing elements, the computer system comprising:

• one or more processors, one or more computer-readable memories and one or more computer-readable, tangible storage devices;
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to divide a reference genome and the genetic sequence of the organism into parts and assign each of the parts of the reference genome and the parts of the genetic sequence of the organism to one of the plurality of computer processing elements;
• within each computer processing element, program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to compare the nucleotides of the assigned part of the genetic sequence of the organism to nucleotides of the assigned part of the reference genome, to find differences where nucleotides of the genetic sequence of the organism are different from the nucleotides of the assigned part of the reference genome, and store surprisal data in a repository, the surprisal data comprising at least a starting location of the differences within the assigned part of the reference genome, and the nucleotides from the genetic sequence of the organism which are different from the nucleotides of the assigned part of the reference genome, discarding sequences of nucleotides that are the same in the genetic sequence of the organism and the assigned part of the reference genome;
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to retrieve the parts of the surprisal data from the repository;
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to combine the parts of the surprisal data from the repository to form a complete set of surprisal data representing the differences between the genetic sequence of the organism and the reference genome;
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to store the complete set of surprisal data in the repository;
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to recreate an entire genome of the organism by:
• retrieving the surprisal data from the repository and dividing the surprisal data into parts;
• retrieving the reference genome from the repository and dividing the reference genome into parts corresponding to the parts of the surprisal data;
• assigning parts of the reference genome and corresponding parts of the surprisal data to each of a plurality of computer processing elements;
• each computer processing element altering the parts of the assigned reference genome based on the corresponding part of the surprisal data, by replacing nucleotides at each location in the assigned parts of the reference genome specified by the corresponding parts of surprisal data with the nucleotides from the genetic sequence of the organism in the surprisal data associated with the location, and storing the altered parts of the reference genome in the repository;
• retrieving the altered parts of the reference genome from the repository;
• and
• combining the altered parts of the reference genome together, resulting in an entire genome of the organism.

A computer system for recreating an entire genome of the organism from a reference genome and surprisal data using a computer having a plurality of computer processing elements, the surprisal data comprising a starting location of the differences within the reference genome, and the nucleotides from the genetic sequence of the organism which are different from the nucleotides of the reference genome, discarding sequences of nucleotides that are the same in the genetic sequence of the organism and the reference genome, the computer system comprising:

• one or more processors, one or more computer-readable memories and one or more computer-readable, tangible storage devices;
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to retrieve surprisal data from a repository and dividing the surprisal data into parts;
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to retrieve the reference genome from the repository and dividing the reference genome into parts corresponding to the parts of the surprisal data;
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to assign parts of the reference genome and corresponding parts of the surprisal data to a plurality of computer processing elements;
• within each computer processing element, program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to alter the parts of the assigned reference genome based on the corresponding part of the surprisal data by replacing nucleotides at each location in the assigned parts of the reference genome specified by the corresponding parts of surprisal data with the nucleotides from the genetic sequence of the organism in the surprisal data associated with the location and store the altered parts of the reference genome in the repository;
• and
• program instructions, stored on at least one of the one or more storage devices for execution by at least one of the one or more processors via at least one of the one or more memories, to retrieve the altered parts of the reference genome in the repository combining the altered parts of the reference genome together, resulting in an entire genome of the organism.