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The plasmid host distribution in NCBI validation dataset. The validation dataset was dominated by the Enterobacterales, Lactobacillales and Pseudomonadales, which make up 76% of the NCBI plasmid hosts.

Journal: bioRxiv

Article Title: PlasmidHostFinder: Prediction of plasmid hosts using random forest

doi: 10.1101/2021.09.27.462084

Figure Lengend Snippet: The plasmid host distribution in NCBI validation dataset. The validation dataset was dominated by the Enterobacterales, Lactobacillales and Pseudomonadales, which make up 76% of the NCBI plasmid hosts.

Article Snippet: The plasmid host models that were trained with the PATRIC plasmids at four different taxonomic levels were validated using plasmids from the National Center for Biotechnology Information (NCBI) Reference Sequence database (RefSeq) ( ).

Techniques: Plasmid Preparation, Biomarker Discovery

Model accuracy for the NCBI plasmids tested with the whole model that was trained with the PATRIC dataset. Each bar shows the number of bacterial orders in the validation data and corresponding model accuracy was color coded. The plot showed that the accuracy of the models changed roughly according to the availability of the host organisms in the training data which was indicated on top of the bars.

Journal: bioRxiv

Article Title: PlasmidHostFinder: Prediction of plasmid hosts using random forest

doi: 10.1101/2021.09.27.462084

Figure Lengend Snippet: Model accuracy for the NCBI plasmids tested with the whole model that was trained with the PATRIC dataset. Each bar shows the number of bacterial orders in the validation data and corresponding model accuracy was color coded. The plot showed that the accuracy of the models changed roughly according to the availability of the host organisms in the training data which was indicated on top of the bars.

Article Snippet: The plasmid host models that were trained with the PATRIC plasmids at four different taxonomic levels were validated using plasmids from the National Center for Biotechnology Information (NCBI) Reference Sequence database (RefSeq) ( ).

Techniques: Biomarker Discovery

The fragment models were validated with the NCBI plasmids. The fragments models that trained with the 500, 1,000 and 1,500 nucleotide (nt) fragments from the PATRIC plasmids were validated with the fragments that sub-sampled from the NCBI plasmids. Similar to the hold-out results, the best performance was obtained with the 1,500 nucleotide fragments and 8 -mers.

Journal: bioRxiv

Article Title: PlasmidHostFinder: Prediction of plasmid hosts using random forest

doi: 10.1101/2021.09.27.462084

Figure Lengend Snippet: The fragment models were validated with the NCBI plasmids. The fragments models that trained with the 500, 1,000 and 1,500 nucleotide (nt) fragments from the PATRIC plasmids were validated with the fragments that sub-sampled from the NCBI plasmids. Similar to the hold-out results, the best performance was obtained with the 1,500 nucleotide fragments and 8 -mers.

Article Snippet: The plasmid host models that were trained with the PATRIC plasmids at four different taxonomic levels were validated using plasmids from the National Center for Biotechnology Information (NCBI) Reference Sequence database (RefSeq) ( ).

Techniques: