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Protocols

rrnDB specifications

Information


Unique identifier OMICS_03212
Name rrnDB
Restrictions to use None
Version 4.3.3
Maintained Yes

Maintainer


  • person_outline Thomas M. Schmidt

Publication for rrnDB

rrnDB citations

 (17)
library_books

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

2018
Appl Environ Microbiol
PMCID: 5861821
PMID: 29427429
DOI: 10.1128/AEM.02627-17

[…] seek to correct for copy number variation using sequence databases and phylogenetic information to give a more accurate picture of the relative abundances of these OTUs. These include Copyrighter (), rrNDB (), functions in the picante R package and pplacer (), and part of the PICRUSt package ().As these techniques are reliant on databases, the same problems are present as for taxonomic identificat […]

library_books

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

2018
Microbiome
PMCID: 5828423
PMID: 29482646
DOI: 10.1186/s40168-018-0420-9

[…] s, yielding 16S GCNs for 6,780 genomes (“high-quality genomes,” Additional file ). The accuracy of these GCNs was further verified through comparison to the Ribosomal RNA Operon Copy Number Database (rrnDB, accessed on June 7, 2017; []) whenever a genome assembly accession was present in the rrnDB (rrnDB attribute “Data source record id”). Across 5,616 high-quality genomes tested, we found an almo […]

library_books

Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias

2018
Genome Biol Evol
PMCID: 5800062
PMID: 29385509
DOI: 10.1093/gbe/evy018

[…] closely related strain (instead of the one included in the original phylogeny). Only completely sequenced genomes (not contigs and scaffolds) were retained. We obtained rRNA copy number data from the rrnDB v5.1 (), or from the IMG database () (downloaded on May 5, 2016). We obtained tRNA GCN directly from GtRNAdb () (downloaded August 13, 2016). For some genomes that were missing in the GtRNAdb, w […]

library_books

Hypersaline sapropels act as hotspots for microbial dark matter

2017
Sci Rep
PMCID: 5522462
PMID: 28733590
DOI: 10.1038/s41598-017-06232-w

[…] ound subtracted data and the LinRegPCR software. The numbers of cells from the numbers of 16 S rRNA genes found in the samples was inferred taking into account the variation in ribosomal RNA operons (rrnDB version 4.3.3). […]

call_split

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China

2017
Microbiome
PMCID: 5517792
PMID: 28724443
DOI: 10.1186/s40168-017-0298-y
call_split See protocol

[…] lization to the absolute copy number of 16S rRNA gene []. The average copy number of 16S rRNA genes per bacterium is currently estimated at 4.1 based on the Ribosomal RNA Operon Copy Number Database (rrnDB version 4.4.4) []. The numbers of bacterial cells were calculated by dividing the copy number of 16S rRNA gene by 4.1, and the ‘relative abundance’ of resistance genes (copies per bacterial cell […]

library_books

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract

2017
Sci Rep
PMCID: 5379200
PMID: 28374781
DOI: 10.1038/srep45840

[…] ained with 16S rRNA training set No. 14 using a bootstrap cutoff of 50%. Subsequently, a gene copy number adjustment for 16S rRNA sequences was performed. The 16S rRNA copy number data is provided by rrnDB website (https://rrndb.umms.med.umich.edu/). A customized script was used to extract and merge abundance data at different taxonomic levels.To minimize the difference of sequencing depth amongst […]

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rrnDB institution(s)
Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA

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