Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

By Qiong Wang, George M. Garrity, James M. Tiedje, James R. Cole. Applied and Environmental Microbiology, 2007

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View Paper: https://www.semanticscholar.org/paper/e3b68ee8cbc57e16a85a2aa79c0befa9a12738c8

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Citations in the corpus

Stool Microbiome and Metabolome Differences between Colorectal Cancer Patients and Healthy Adults (2013, positive): “org) and the naı̈ve Baysian classifier [23] embedded in Mothur.”
Combined amendment of immobilizers and the plant growth-promoting strain Burkholderia phytofirmans PsJN favours plant growth and reduces heavy metal uptake (2015, methodology): “8 (Wang et al., 2007) against the last version of the Greengenes database (08/2013) (McDonald et al.”
Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe (2014, methodology): “Taxonomy was assigned using the Ribosomal Database Project classifier (Wang et al., 2007).”
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics (2016, methodology): “Taxonomy was then assigned using the RDP classifier, using the UCLUST method (Wang et al., 2007).”
Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees (2008, neutral): “(44) at the Ribosome Database Project II”
Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota (2017, methodology): “Representative sequences from each OTU were aligned using PyNAST (a python-based implementation of NAST in QIIME) 39 and taxonomy was assigned using the Greengenes database (v. 13_8) 42 and the RDP classi fi er 43 .”
Soil microbial community under a nurse-plant species changes in composition, biomass and activity as the nurse grows (2013, methodology): “Taxonomic assignation of the sequences was performed using the RDP naïve Bayesian classifier (Wang et al., 2007) at a confidence level of 50% (recommended for short sequences, Claesson et al.”
Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil (2020, methodology): “The RDP 16S training set and the RefSeq 16S reference sequence collection were used for classification.”
Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome (2008, result): “in SI give details). These results also showed that neither reference database introduced a major artificial “community” shift; rather, both correctly reflected the test set's “community” structure. In addition, none of the ribo-tags were taxonomically wrongly assigned. Even with a ribo-tag length o”