Methods, compounds and systems for detecting a microorganism in a sample

摘要

Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.

主权项

1. A computer implemented method to identify a set of probe polynucleotides suitable for detecting a set of target microorganisms, the method comprising a processor:
receiving as input the set of target microorganisms; receiving as input a set of rules to be satisfied by target sequences and related to hybridization of the target sequences to complementary polynucleotides; identifying a set of target polynucleotides by selecting one or more target polynucleotides, each target polynucleotide comprised in at least one microorganism of the target microorganisms, each target polynucleotide comprising a target sequence satisfying to the set of rules; and identifying the set of probe polynucleotides by reverse complementing one or more of the target sequences of the target polynucleotides of the identified set of target polynucleotides, wherein identifying a set of target polynucleotides is performed by
identifying a first target polynucleotide and a second target polynucleotide in at least one microorganism of the set of target microorganisms, wherein the second target polynucleotide comprises a target sequence satisfying to a rule requiring detection of said at least one microorganism performed by the second target polynucleotide in combination with the first target polynucleotide;identifying one of the first and the second target polynucleotides in one or more additional target microorganisms, with the one or more additional target microorganisms different from the first target microorganism; andidentifying one or more additional target polynucleotides in the one or more additional target microorganisms, wherein the one or more additional target polynucleotides comprise one or more additional target sequences satisfying to a rule requiring detection of said one or more additional target microorganisms performed by said one or more additional target polynucleotides in combination with the one of the first target polynucleotide and the second target polynucleotide,wherein the set of probe polynucleotides includes a first pair of probe polynucleotides identified by complementing target sequences of the first target polynucleotide or the second target polynucleotide and a second pair of probe polynucleotides identified by complementing target sequences of the one of the first target polynucleotide and the second target polynucleotide and target sequences of the one or more additional target polynucleotides;wherein identifying a first target polynucleotide and a second target polynucleotide in at least one microorganism of the set of target microorganisms is performed byi) identifying a first set of candidate polynucleotides present in at least one of the target microorganisms;ii) sorting the candidate polynucleotides of the first set by number of target microorganisms in which they occur;iii) identifying second and third sets of candidate polynucleotides, said second and third sets comprising polynucleotides lying within a distance range of the polynucleotides of the first set of candidate polynucleotides, the second set comprising polynucleotides lying upstream of the first set, and the third set comprising polynucleotides lying downstream of the first set;iv) sorting the candidate polynucleotides of the second and third sets by number of target microorganisms in which they occur;v) selecting a most frequently occurring polynucleotide from the first set as the first target polynucleotide and a most frequently occurring polynucleotide from the second or third sets as the second target polynucleotide.