rrndb: the Ribosomal RNA Operon Copy Number Database

By J. Klappenbach, P. Saxman, James R. Cole, Thomas M. Schmidt. Nucleic Acids Res., 2001

1,125 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/638f10c6cc396907b98424621f6420a4287d342f

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Citations in the corpus

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea (2008, background): “information on 16S rRNA-encoding genes in the first iteration of the rrnDB (10).”
A Patchwork of Streptomyces Species Isolated from Potato Common Scab Lesions in North America (2009, result): “…have six copies of the ribosomal gene repeat and there are examples of sequence polymorphisms among the rDNA gene copies in a few bacterial species (Klappenbach et al. 2001), but this is infrequent and was not the case for the three published Streptomyces genomes (Bentley et al. 2002; Ikeda et al.…”
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies (2006, neutral): “1 ribosomal operons per bacterial genome (21).”
Stream Biofilm Responses to Flow Intermittency: From Cells to Ecosystems (2016, background): “Perennial pools, leaf litter packs, or even subsuperficial sediments, may temporarily offer wet environments, therefore acting as refuges for microbes.”
Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community (2013, background): “php) (Klappenbach et al., 2001).”
Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays (2005, background): “There are a number of reasons for this: DNA extraction bias may alter the estimated abundances of certain groups (16), heterogeneity in ribosomal operon number (11, 30) may affect relative estimates of group abundances, and the tested qPCR assays do not necessarily amplify rRNA genes belonging to al”
Soil Microbial Community Analysis Using Denaturing Gradient Gel Electrophoresis (2007, background): “The number of PCR products can be biased to specifi c groups (Baker and Cowan, 2004) or overestimated because of multiple rDNA copies per genome (Klappenbach et al., 2001).”
Temporal variation and detection limit of an estuarine bacterioplankton community analyzed by denaturing gradient gel electrophoresis (DGGE) (2006, background): “At the time, the Ribosomal RNA Operon Copy Number Database (rrndb) (Klappenbach et al. 2001) contained 502 entries, with 259 genome sizes and rRNA operon copy numbers available.”
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development (2014, background): “Unlike most bacterial and archaeal genes, the rRNA operon is frequently found in multiple copies, from 1–15 in bacteria and 1–4 in archaea (1).”
Toward a Census of Bacteria in Soil (2006, background): “Considering potential intragenomic differences between copies of 16S rRNA genes and errors due to sequencing and alignment [ 29 ,30], the 0.03 cutoff is also a pragmatic choice since it probably represents the most stringent OTU definition that is practically obtainable using 16S rRNA genes.”