Evaluation of the RDP classifier accuracy using 16S rRNA gene variable regions
Joint Authors
Source
Issue
Vol. 1, Issue 2012 (31 Dec. 2012), pp.1-5, 5 p.
Publisher
Publication Date
2012-12-31
Country of Publication
Egypt
No. of Pages
5
Main Subjects
Abstract EN
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).
American Psychological Association (APA)
Vilo, Claudia& Dong, Qunfeng. 2012. Evaluation of the RDP classifier accuracy using 16S rRNA gene variable regions. Metagenomics،Vol. 1, no. 2012, pp.1-5.
https://search.emarefa.net/detail/BIM-686007
Modern Language Association (MLA)
Vilo, Claudia& Dong, Qunfeng. Evaluation of the RDP classifier accuracy using 16S rRNA gene variable regions. Metagenomics Vol. 1 (2012), pp.1-5.
https://search.emarefa.net/detail/BIM-686007
American Medical Association (AMA)
Vilo, Claudia& Dong, Qunfeng. Evaluation of the RDP classifier accuracy using 16S rRNA gene variable regions. Metagenomics. 2012. Vol. 1, no. 2012, pp.1-5.
https://search.emarefa.net/detail/BIM-686007
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references : p. 5
Record ID
BIM-686007