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American Society for Microbiology, Applied and Environmental Microbiology, 7(72), p. 5069-5072, 2006

DOI: 10.1128/aem.03006-05

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

Journal article published in 2006 by Todd Z. DeSantis, Philip Hugenholtz ORCID, Neils Larsen, Mark Rojas, Eoin L. Brodie ORCID, Keith Keller, Thomas Huber, Daniel Dalevi, Ping Hu, Gary L. Andersen
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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 .