Classifier

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The RDP naïve Bayesian Classifier offers two hierarchy models for 16S rRNA and Fungal LSU genes. The current hierarchy model used by the 16S rRNA Classifier comes from that proposed in the new phylogenetically consistent higher-order bacterial taxonomy with some minor changes for lineage with few cultivated members.

The Fungal LSU Classifier (large subunit rRNA gene) hierarchy model and training set were provided by Andrea Porras-Alfaro, Gary Xie, and Cheryl Kuske (supported through a DOE Science Focus Area grant to Los Alamos National Laboratory). The fungal training set consists of 8506 high-quality public Sanger sequences spanning the first 1400 bp of the LSU gene. This dataset and taxonomic hierarchy were hand-curated for taxonomic accuracy. Their results showed the Fungal LSU Classifier was computationally faster (over 460 fold) than BLASTN and provided equal or superior classification accuracy [K-L. Liu, C. R. Kuske, A. Porras-Alfaro, S. Eichorst, G. Xie. 2011. Accurate, rapid taxonomic classification of fungal large subunit rRNA genes].

From the highest to the lowest, the major formal taxonomic ranks are: domain, phylum, class, order, family and genus. There are occasional intermediate ranks such as “subclass” and “suborder”.

The source code of RDP Classifier is freely available from http://sourceforge.net/projects/rdp-classifier/ and https://github.com/rdpstaff.

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