Appl Environ Microbiol. 2006 Jul;72(7):5069-72.

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL.

Source

Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA.

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.

PMID:: 16820507; [PubMed - indexed for MEDLINE]
PMCID:: PMC1489311

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Research Support, U.S. Gov't, Non-P.H.S.

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Substances

RNA, Ribosomal, 16S

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