RDP Classifier statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RDP Classifier
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Tool usage distribution map

This map represents all the scientific publications referring to RDP Classifier per scientific context
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Protocols

RDP Classifier specifications

Information


Unique identifier OMICS_18112
Name RDP Classifier
Alternative name Ribosomal Database Project Classifier
Interface Web user interface
Restrictions to use None
Input data A sequence with at least 50 bases to get a good classification result.
Input format FASTA, GENBANK, EMBL
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline James Cole

Information


Unique identifier OMICS_18112
Name RDP Classifier
Alternative name Ribosomal Database Project Classifier
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data A sequence with at least 50 bases to get a good classification result.
Input format FASTA, GENBANK, EMBLLinux
Programming languages PHP
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.10.2
Stability Stable
Source code URL https://codeload.github.com/rdpstaff/classifier/tar.gz/2.10.2
Maintained Yes

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Maintainer


  • person_outline James Cole

Publication for Ribosomal Database Project Classifier

RDP Classifier citations

 (1941)
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Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial

2018
MBio
PMCID: 5964358
DOI: 10.1128/mBio.02392-17
call_split See protocol

[…] y analysis, including principal-component analysis (PCA) and principal-coordinate analysis (PCoA) based on Bray-Curtis, UniFrac, and Jaccard distances. The taxonomy of each OTU was assigned online by RDP Classifier (RDP Naive Bayesian rRNA Classifier version 2.10) with a bootstrap cutoff of 80%. […]

library_books

American Gut: an Open Platform for Citizen Science Microbiome Research

2018
mSystems
PMCID: 5954204
DOI: 10.1128/mSystems.00031-18

[…] e estimation strategy described in reference to identify reasonable placements for sequence fragments within an existing phylogeny and alignment. Taxonomy was assigned using an implementation of the RDP classifier () as implemented in QIIME2 (). Multiple rarefactions were computed, with the minimum being 1,250 sequences per sample with the analyses using the 1,250-sequence set except where noted […]

library_books

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum

2018
Microbiome
PMCID: 5952429
PMID: 29764499
DOI: 10.1186/s40168-018-0472-x

[…] se OTU sequences, and 10,000 randomly chosen sequences were used to construct the OTU abundance table. Additionally, OTU sequences underwent taxonomic annotation using the ribosomal database project (RDP) classifier [] and training set 16 provided on the RDP website (https://rdp.cme.msu.edu). The cut-off for annotation was set to a classification score of 0.8, assigning each OTU to the lowest taxo […]

library_books

Microbial community analysis and biodeterioration of waterlogged archaeological wood from the Nanhai No. 1 shipwreck during storage

2018
Sci Rep
PMCID: 5940862
PMID: 29740020
DOI: 10.1038/s41598-018-25484-8

[…] is was performed against the Unite database (v. 20140703) in QIIME (v. 1.7.0) to taxonomically annotate OTUs. For bacterial OTUs, the Greengenes database (http://greengenes.lbl.gov) was used with the RDP classifier (v. 2.2) algorithm for taxonomic annotation. Multiple sequence alignments were then conducted using MUSCLE (v. 3.8.31) in order to compare OTU distributions among samples. Read numbers […]

call_split

Research on oral microbiota of monozygotic twins with discordant caries experience in vitro and in vivo study

2018
Sci Rep
PMCID: 5940813
PMID: 29740156
DOI: 10.1038/s41598-018-25636-w
call_split See protocol

[…] ltered by QIIME (version 1.9.1). Operational Taxonomic Units (OTUs) were clustered with 98.5% similarity cutoff using UPARSE (version 7.1). The taxonomy of each 16S rRNA gene sequence was analyzed by Ribosomal Database Project Classifier (http://rdp.cme.msu.edu/) against the Human Oral Microbiome Database with confidence threshold of 70%. Alpha diversity indices (Shannon index, Simpson index) and […]

library_books

Near full length 16S rRNA gene next generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae

2018
Microbiome
PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…] using the UCLUST algorithm [], as implemented in QIIME using the pick_open_reference_otus.py command. Default settings were used, with the exception of picking OTUs at 99% similarity and training the RDP classifier [, ] against the Greengenes 16S rRNA gene reference database version 13_5 preclustered at 99% []. The default settings included a minimum of two sequences per OTU. Representative OTU se […]


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RDP Classifier institution(s)
Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
RDP Classifier funding source(s)
Supported by the Office of Science, U.S. Department of Energy, grant DE-FG02-99ER62848, and the National Science Foundation, grant DBI-0328255.

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