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PLoS One. 2015 Feb 3;10(2):e0116106. doi: 10.1371/journal.pone.0116106. eCollection 2015.

16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets.

Author information

1
MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh, India.
2
MetaInformatics Laboratory, Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh, India; Department of Physics, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh, India.

Abstract

The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome sequencing technologies, the focus has shifted towards the sequencing of hypervariable regions of 16S rRNA gene instead of full length gene sequencing. Therefore, 16S Classifier is developed using a machine learning method, Random Forest, for faster and accurate taxonomic classification of short hypervariable regions of 16S rRNA sequence. It displayed precision values of up to 0.91 on training datasets and the precision values of up to 0.98 on the test dataset. On real metagenomic datasets, it showed up to 99.7% accuracy at the phylum level and up to 99.0% accuracy at the genus level. 16S Classifier is available freely at http://metagenomics.iiserb.ac.in/16Sclassifier and http://metabiosys.iiserb.ac.in/16Sclassifier.

PMID:
25646627
PMCID:
PMC4315456
DOI:
10.1371/journal.pone.0116106
[Indexed for MEDLINE]
Free PMC Article

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