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US 12,646,587 B2Granted
Determining signature snippets that identify nucleic acid sequences of biological organisms
AssigneeRtx Bbn Technologies, Inc.
InventorsJacob Stuart Michael Beal, Daniel Wyschogrod, Steven Wayne Jilcott, Jr.
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Abstract
Disclosed techniques include generating a first set of sequence snippets from a set of nucleic acid sequences having a first trait; generating a second set of second sequence snippets from a set of nucleic acid sequences having a second trait; identifying a third set of sequence snippets categorized as being of a particular type; and filtering the first set of sequence snippets and the second set of sequence snippets to remove at least one sequence snippet in the third set of sequence snippets.
Claims20
A method comprising:
- determining, by a computing system including one or more computing devices having one or more hardware processors and memory, a minimum number of benign snippets to be included in a plurality of benign snippets, the minimum number sufficient to yield a false positive rate below a threshold;
- generating, by the computing system, a first plurality of sequence snippets from a first plurality of nucleic acid sequences corresponding to one or more first biological organisms having a first trait;
- generating, by the computing system, a second plurality of sequence snippets from a second plurality of nucleic acid sequences corresponding to one or more second biological organisms having a second trait;
- identifying, by the computing system, a third plurality of sequence snippets categorized as benign snippets, the third plurality of sequence snippets having at least the minimum number of benign snippets such that the false positive rate is below the threshold;
- filtering, by the computing system, the first plurality of sequence snippets by removing at least one of the third plurality of sequence snippets from the first plurality of sequence snippets such that first candidate signature snippets are produced, the first candidate signature snippets including a portion of the first plurality of sequence snippets and corresponding to the one or more first biological organisms;
- and
- filtering, by the computing system, the second plurality of sequence snippets by removing at least one of the third plurality of sequence snippets from the second plurality of sequence snippets such that second candidate signature snippets are produced, the second candidate signature snippets including a portion of the second plurality of sequence snippets and corresponding to the one or more second biological organisms.
4 more elements
One or more non-transitory computer-readable media storing instructions that, when executed by one or more processors, is configured to cause the one or more processors to perform operations comprising:
- determining a minimum number of benign snippets to be included in a plurality of benign snippets, the minimum number sufficient to yield a false positive rate below a threshold;
- generating a first plurality of sequence snippets from a first plurality of nucleic acid sequences corresponding to one or more first biological organisms having a first trait;
- generating a second plurality of sequence snippets from a second plurality of nucleic acid sequences corresponding to one or more second biological organisms having a second trait;
- identifying a third plurality of sequence snippets categorized as being of a particular type;
- filtering the first plurality of sequence snippets by removing at least one of the third plurality of sequence snippets from the first plurality of sequence snippets such that first candidate signature snippets are produced, the first candidate signature snippets including a portion of the first plurality of sequence snippets and corresponding to the one or more first biological organisms;
- and
- filtering the second plurality of sequence snippets by removing at least one of the third plurality of sequence snippets from the second plurality of sequence snippets such that second candidate signature snippets are produced, the second candidate signature snippets including a portion of the second plurality of sequence snippets and corresponding to the one or more second biological organisms.
4 more elements
A system comprising:
- at least one device including a hardware processor;
- and
- memory storing computer-readable instructions that, when executed by the hardware processor, is configured to cause the hardware processor to perform operations comprising:
- determining a minimum number of benign snippets to be included in a plurality of benign snippets, the minimum number sufficient to yield a false positive rate below a threshold;
- generating a first plurality of sequence snippets from a first plurality of nucleic acid sequences corresponding to one or more first biological organisms having a first trait;
- generating a second plurality of sequence snippets from a second plurality of nucleic acid sequences corresponding to one or more second biological organisms having a second trait;
- identifying a third plurality of sequence snippets categorized as benign snippets, the third plurality of sequence snippets having at least the minimum number of benign snippets such that the false positive rate is below the threshold;
- filtering the first plurality of sequence snippets by removing at least one of the third plurality of sequence snippets from the first plurality of sequence snippets such that first candidate signature snippets are produced, the first candidate signature snippets including a portion of the first plurality of sequence snippets and corresponding to the one or more first biological organisms;
- and
- filtering the second plurality of sequence snippets by removing at least one of the third plurality of sequence snippets from the second plurality of sequence snippets such that second candidate signature snippets are produced, the second candidate signature snippets including a portion of the second plurality of sequence snippets and corresponding to the one or more second biological organisms.
7 more elements
Dependencies are inferred from the claim text.