Evaluation of the RDP Classifier Accuracy Using 16S rRNA Gene Variable Regions

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This article uses full-length 16S rRNA gene alignments from the SILVA database to simulate the PCR products of the combined variable regions.

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5 p.

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Vilo, Claudia A. & Dong, Qunfeng March 12, 2012.

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This article is part of the collection entitled: UNT Scholarly Works and was provided by the UNT College of Engineering to the UNT Digital Library, a digital repository hosted by the UNT Libraries. It has been viewed 244 times, with 7 in the last month. More information about this article can be viewed below.

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This article uses full-length 16S rRNA gene alignments from the SILVA database to simulate the PCR products of the combined variable regions.

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5 p.

Notes

Abstract: The RDP Classifier is a widely used bioinformatic
program that performs taxonomic classification of
16S rRNA gene sequences. However, the accuracy of the
program is not clear when it is applied to common PCR
products of the 16S rRNA variable regions, which are
heavily used in microbiome projects. In this study, fulllength
16S rRNA gene alignments from the SILVA database
were used to simulate the PCR products of the combined
variable regions (i.e., V1–V3, V3–V5, and V6–V9). The
classification accuracies obtained from RDP Classifier were
evaluated for each of the simulated 16S rRNA regions, at
different confidence score thresholds. Although minor bias
was observed, the RDP Classifier achieved overall similar
and accurate classification results when using the combined
variable regions of the 16S rRNA gene, i.e., V1–V3, V3–
V5, and V6–V9. Additional analysis showed that V2 and
V4 were the most accurate among individual regions (i.e.,
V1 to V9).

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  • Metagenomics, 1, Ashdin Publishing, March 12, 2012, pp. 1-5

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  • Publication Title: Metagenomics
  • Volume: 1
  • Peer Reviewed: Yes

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UNT Scholarly Works

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  • March 12, 2012

Added to The UNT Digital Library

  • April 25, 2019, 9:08 p.m.

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  • Dec. 12, 2023, 2:07 p.m.

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Vilo, Claudia A. & Dong, Qunfeng. Evaluation of the RDP Classifier Accuracy Using 16S rRNA Gene Variable Regions, article, March 12, 2012; Cairo, Egypt. (https://digital.library.unt.edu/ark:/67531/metadc1475536/: accessed February 28, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT College of Engineering.

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