Cited by 10,891Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyEnvironmental DNA in Biodiversity Studies

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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

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DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., Andersen, G. L.·2006·Applied and Environmental Microbiology

DOI 10.1128/aem.03006-05

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Abstract

A 16S rRNA gene database ( http://greengenes.lbl.gov ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria .

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Authors: DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L.
Affiliations: Lawrence Berkeley National Laboratory (US)
Joint Genome Institute (US)
Danish Genome Institute, Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
Baylor University (US)
University of California, Berkeley (US)
The University of Queensland (AU)
Chalmers University of Technology (SE)
Corresponding author: Andersen, G. L.
ORCID: DeSantis, T. Z.
Hugenholtz, P.
Larsen, N.
Brodie, E. L.
Huber, T.
Andersen, G. L.
Venue: Applied and Environmental Microbiology
Publisher: American Society for Microbiology
Published: 2006-07
Volume: 72
Issue: 7
Pages: 5069-5072
ISSN: 0099-2240 (ISSN-L)
1098-5336
DOI: 10.1128/aem.03006-05
OpenAlex: W1988925586
Semantic Scholar: 41abf43dc718e271299457bce65bccfe3feeb9d6
Cited by: 10,891
References: 33
Citations by year: 2026: 220 · 2025: 384 · 2024: 545 · 2023: 576 · 2022: 741 · 2021: 1058 · 2020: 1148 · 2019: 1084 · 2018: 1054 · 2017: 964 · 2016: 770 · 2015: 561 · 2014: 441 · 2013: 317 · 2012: 296
FWCI: 36.66
Type: journal article
Language: en
Open access: green
europepmc.org
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Applied and Environmental Microbiology (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed (publishedVersion)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
University of North Texas Digital Library (University of North Texas) (submittedVersion)
ANU Open Research (Australian National University) (submittedVersion)
eScholarship (California Digital Library) (submittedVersion)
Chalmers Publication Library (Chalmers University of Technology) (submittedVersion)
Chalmers Research (Chalmers University of Technology) (submittedVersion)
Lawrence Berkeley National Laboratory
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Keywords: Greengenes, chimeric sequences, taxonomic classification, sequence alignment, angiotensin receptor blockers, bacterial taxonomy, archaeal taxonomy
MeSH terms: Archaea, Bacteria, Recombination, Genetic, RNA, Ribosomal, 16S, Software, Reproducibility of Results, Polymerase Chain Reaction, Sequence Alignment, Genes, rRNA, Databases, Nucleic Acid

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