Greengenes, a Chimera-checked 16S rRNA gene database and workbenchcompatible with ARB

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that in congruent taxonomic nomenclature exists among curators even...

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Bibliographic Details
Published in:Applied and environmental microbiology 2006-04, Vol.72 (7)
Main Authors: DeSantis, Todd Z., Hugenholtz, Philip, Larsen, Neils, Rojas,Mark, Brodie, Eoin L., Keller, Keith, Huber, Thomas, Dalevi, Daniel, Hu,Ping, Andersen, Gary L.
Format: Article
Language:English
Subjects:
16S rRNA bacteria archaea taxonomy chimera
BACTERIA
BASIC BIOLOGICAL SCIENCES
CHIMERAS
CLASSIFICATION
ENVIRONMENTAL SCIENCES
GENES
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Summary:A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that in congruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3 percent of environmental sequences and 0.2 percent of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.
ISSN:0099-2240
1098-5336
DOI:10.1128/AEM.03006-05