Patent Document ID: 10042976
Application ID: 13934029
Patent Flag: 1

Claim One:
1. A computer-implemented method of identifying a microorganism in a sample, the method comprising: creating a reference word database comprising billions of reference words, wherein the reference word database is generated by an in silica process comprising: (i) fragmenting at least first nucleic acid sequences derived from a first reference genome of a first known microorganism and at least second nucleic acid sequences derived from a second reference genome of a second known microorganism into reference words, wherein at least some of the reference words comprise a nucleic acid sequence greater than or equal to 18 letters and less than or equal to 27 letters, and each reference word is associated with a species, sub-species or strain of a known microorganism from which each reference word was derived; (ii) cataloging the reference words into a plurality of lists of reference words, wherein the plurality of lists of reference words comprise a first list of reference words associated with the first known microorganism and a second list of reference words associated with the second known microorganism, and (iii) storing the plurality of lists of reference words organized as a phylogenetic tree in the reference word database; storing the reference word database in a taxonomy cache that includes the Plurality of list of reference words; creating a plurality of sample sequence words by an in silica process comprising fragmenting a mixture of nucleic acid sequences derived from a plurality of genomes each corresponding to an unidentified microorganism in a sample into sample sequence words, wherein at least some of the sample sequence words comprise a nucleic acid sequence greater than or equal to 18 letters and less than or equal to 27 letters that corresponds to an unidentified microorganism in the sample; comparing the sample sequence words to the reference words in the reference word database; filtering out at least a portion of the reference word database in the taxonomy cache to eliminate non-matching portions of the phylogenetic tree based on the comparison, thereby reducing a decision space in the taxonomy cache for identifying one or more microorganisms in the sample, the filtered reference word database including the first list of reference words and the second list of reference words; determining a first number of matches between the first list of reference words associated with the first known microorganism and the sample sequence words; determining a second number of matches between the second list of reference words associated with the second known microorganism and the sample sequence words; determining that the species, sub-species or strain of the first known microorganism is present in the sample based on the first number of matches; and determining that the species, sub-species or strain of the second known microorganism is present in the sample based on the second number of matches.