Electronic methods and systems for microorganism characterization
Inventors
Fry, Stephen E. • Ellis, Jeremy
Assignees
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Publication Number
US-9589101-B2
Publication Date
2017-03-07
Expiration Date
Abstract
Systems and methods to characterize one or more microorganisms or DNA fragments thereof are disclosed. Exemplary methods and systems use comparison of DNA sequencing information to information in one or more databases to characterize the one or more microorganism or DNA fragments thereof. Exemplary systems and methods can be used in a clinical setting to provide rapid analysis of microorganisms that may be a cause of infection.
Core Innovation
The invention provides a computer-implemented method of characterizing one or more microorganisms from digital DNA sequences. A file comprising one or more digital DNA sequences is accessed, selected, and segmented so that each file portion can be processed by a processing core. The method partitions each microorganism-corresponding digital DNA sequence into one or more first portions for a first alignment stage.
The method performs a first set of alignments by comparing the one or more first portions to information stored in a first database, and determines sequence portions from among the one or more first portions that have an alignment match to the first database information. Each digital DNA sequence is then segmented into one or more second portions using a window of a window size, after which iterative alignment actions are performed.
For each DNA sequence, the method performs a second set of alignments by comparing the one or more second portions to information stored in a second database, and determines whether the comparison failed to produce at least one alignment match between any second portion and information stored in the second database. When the comparison fails and the window size has not decreased beyond a designated stringency level, the window size is decreased, the second portions are re-segmented using the decreased window size, and the second alignment actions are repeated. One or more microorganisms are characterized based on a first result from the first database alignment match determination and a second result from the second-database alignment actions.
Claims Coverage
The provided material identifies two independent claims. Each independent claim covers a computer-implemented microorganism characterization workflow that combines first-database matching with a second-database iterative alignment process that decreases window size up to a designated stringency level.
Two-stage alignment with iterative window-size refinement
Performing a first set of alignments by comparing one or more first portions to information stored in a first database; determining sequence portions that have an alignment match; segmenting each DNA sequence into one or more second portions using a window of a window size; performing a second set of alignments by comparing the one or more second portions to information stored in a second database; determining whether the comparison failed to produce at least one alignment match; when the comparison failed and the window size has not decreased beyond a designated stringency level, decreasing the window size, repeating the segmentation into second portions using the decreased window size, and repeating the set of iterative alignment actions; and characterizing one or more microorganisms based on a first result from the first database and a second result from the second-database alignment actions.
Automatic characterization from detecting a sequence run
Detecting a sequence run that generates a digital DNA sequence of one or more microorganisms; selecting a digital file comprising one or more digital DNA sequences where each corresponds to a microorganism; dividing the digital DNA sequences into file portions processed by a processing core; segmenting each digital DNA sequence into one or more portions; performing a first set of alignments by comparing the one or more portions to information stored in one or more databases; determining sequence portions that have an alignment match; segmenting each DNA sequence into one or more second portions using a window of a window size; performing a set of iterative alignment actions including a second set of alignments against a second database, determining failure to produce at least one alignment match, and when the comparison failed and the window size has not decreased beyond a designated stringency level, decreasing the window size, repeating segmentation, and repeating the iterative alignment actions; and characterizing one or more microorganisms based on a first result from the determination at the first stage and a second result from the second-database alignment actions.
Across both independent claims, characterization is based on alignment results from a first database stage and an iterative second database stage that decreases a window size up to a designated stringency level when alignment matches are not produced.
Stated Advantages
Documented Applications
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