Method for screening important characteristic genes related to bacterial drug resistance phenotype based on machine learning
A feature gene, machine learning technology, applied in the field of gene sequencing
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Embodiment 1
[0085] Embodiment 1 Design optimization of this application
[0086] As mentioned in the background technology section of this application, most of the existing bacterial resistance screening studies focus on the screening of single nucleotide polymorphism (SNP), insertion / deletion (Indel) or k-mer characteristics at the core genome level, But in addition to these features, it is also very important to screen for important non-core drug resistance genes associated with drug resistance phenotypes.
[0087] figure 1 This is the design idea of this application, and based on this idea, this example designs a specific method for optimizing drug resistance screening. The establishment process of this application is shown by taking model selection as an example.
[0088] In the association analysis between genotype and drug susceptibility result data, this application uses the GLM generalized linear model (R language glm(), stepAIC() commands), Lasso regression model (R language ...
Embodiment 2
[0097] Example 2 Screening and verification of important characteristic genes related to carbapenem and cephalosporin resistance in Klebsiella pneumoniae
[0098] Step 1. From the public database, search and download the Klebsiella pneumoniae strain genome and its corresponding antibiotic susceptibility test result data.
[0099] Download from the NCBI NDARO database: Open the website https: / / www.ncbi.nlm.nih.gov / pathogens / isolates, enter "Klebsiella pneumoniae" in the search bar to retrieve Klebsiella pneumoniae information, and then in the Matched Isolates sub-window, click "Choose columns" select "AST pheotypes" to display the information in this column, then download the tabular data of the entire window, sort out the pulmonary strains with drug susceptibility test result data, according to the Assembly ID information, from NCBI's genome database (ftp: / / ftp.ncbi.nlm.nih.gov / genomes) to download genome sequences in bulk.
[0100] Download from the PATRIC platform database...
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