Electronic Methods And Systems For Microorganism Characterization

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.

1 - 20 . (canceled) 
     
     
         21 . A computer-implemented method of identifying one or more microorganisms or DNA fragments thereof, the method comprising:
 accessing, at a computer system, a DNA sequence data set;   performing an iterative alignment process using the DNA sequence data, wherein the iterative alignment process comprises sequentially generating alignment results based on the DNA sequence data set and reference sequences in a given database corresponding to the iteration until an alignment criterion for a given iteration is satisfied based on a corresponding alignment result;   predicting, based on the iterative alignment process, that the sample includes one or more microorganisms; and   outputting an identification of the one or more microorganisms.   
     
     
         22 . The computer-implemented method of identifying one or more microorganisms or DNA fragments thereof of  claim 21 , wherein the iterative alignment process is configured to, upon determining that an alignment criterion for a particular iteration is not satisfied based on a corresponding alignment result, revert to aligning the DNA sequence data with one or more reference sequences in a given database corresponding to a previous iteration. 
     
     
         23 . The computer-implemented method of identifying one or more microorganisms or DNA fragments thereof of  claim 21 , wherein the iterative alignment process is configured to, upon determining that an alignment criterion for a particular iteration is not satisfied based on a corresponding alignment result, determining that the DNA sequence data aligns with one or more reference sequences in a given database corresponding to a previous iteration. 
     
     
         24 . The computer-implemented method of identifying one or more microorganisms or DNA fragments thereof  claim 21 , wherein—for a given iteration—it is determined that the alignment criterion is not satisfied when a maximum alignment score between the DNA sequence data set and multiple corresponding reference data sets is below a predetermined threshold. 
     
     
         25 . The computer-implemented method of identifying one or more microorganisms or DNA fragments thereof  claim 21 , wherein a quantity of the reference sequences in the given databases increases across a first two of the iterations. 
     
     
         26 . The computer-implemented method of identifying one or more microorganisms or DNA fragments thereof  claim 21 , wherein the one or more microorganisms includes a fungus. 
     
     
         27 . The computer-implemented method of identifying one or more microorganisms or DNA fragments thereof  claim 21 , wherein the one or more microorganisms includes a bacterium. 
     
     
         28 . A system comprising:
 one or more data processors; and   a non-transitory computer readable storage medium containing instructions which when executed on the one or more data processors, cause the one or more data processors to perform actions including:
 accessing, at a computer system, a DNA sequence data set; 
 performing an iterative alignment process using the DNA sequence data, wherein the iterative alignment process comprises sequentially generating alignment results based on the DNA sequence data set and reference sequences in a given database corresponding to the iteration until an alignment criterion for a given iteration is satisfied based on a corresponding alignment result; 
 predicting, based on the iterative alignment process, that the sample includes one or more microorganisms; and 
 outputting an identification of the one or more microorganisms. 
   
     
     
         29 . The system of  claim 28 , wherein the iterative alignment process is configured to, upon determining that an alignment criterion for a particular iteration is not satisfied based on a corresponding alignment result, revert to aligning the DNA sequence data with one or more reference sequences in a given database corresponding to a previous iteration. 
     
     
         30 . The system of  claim 28 , wherein the iterative alignment process is configured to, upon determining that an alignment criterion for a particular iteration is not satisfied based on a corresponding alignment result, determining that the DNA sequence data aligns with one or more reference sequences in a given database corresponding to a previous iteration. 
     
     
         31 . The system of  claim 28 , wherein—for a given iteration—it is determined that the alignment criterion is not satisfied when a maximum alignment score between the DNA sequence data set and multiple corresponding reference data sets is below a predetermined threshold. 
     
     
         32 . The system of  claim 28 , wherein a quantity of the reference sequences in the given databases increases across a first two of the iterations. 
     
     
         33 . The system of  claim 28 , wherein the one or more microorganisms includes a fungus. 
     
     
         34 . The system of  claim 28 , wherein the one or more microorganisms includes a bacterium. 
     
     
         35 . A computer-program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform actions including:
 accessing, at a computer system, a DNA sequence data set;   performing an iterative alignment process using the DNA sequence data, wherein the iterative alignment process comprises sequentially generating alignment results based on the DNA sequence data set and reference sequences in a given database corresponding to the iteration until an alignment criterion for a given iteration is satisfied based on a corresponding alignment result;   predicting, based on the iterative alignment process, that the sample includes one or more microorganisms; and   outputting an identification of the one or more microorganisms.   
     
     
         36 . The computer-program product of  claim 35 , wherein the iterative alignment process is configured to, upon determining that an alignment criterion for a particular iteration is not satisfied based on a corresponding alignment result, revert to aligning the DNA sequence data with one or more reference sequences in a given database corresponding to a previous iteration. 
     
     
         37 . The computer-program product of  claim 35 , wherein the iterative alignment process is configured to, upon determining that an alignment criterion for a particular iteration is not satisfied based on a corresponding alignment result, determining that the DNA sequence data aligns with one or more reference sequences in a given database corresponding to a previous iteration. 
     
     
         38 . The computer-program product of  claim 35 , wherein—for a given iteration—it is determined that the alignment criterion is not satisfied when a maximum alignment score between the DNA sequence data set and multiple corresponding reference data sets is below a predetermined threshold. 
     
     
         39 . The computer-program product of  claim 35 , wherein a quantity of the reference sequences in the given databases increases across a first two of the iterations. 
     
     
         40 . The computer-program product of  claim 35 , wherein the one or more microorganisms includes a fungus.