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

TZ DeSantis, P Hugenholtz, N Larsen… - Applied and …, 2006 - Am Soc Microbiol
TZ DeSantis, P Hugenholtz, N Larsen, M Rojas, EL Brodie, K Keller, T Huber, D Dalevi, P Hu…
Applied and environmental microbiology, 2006Am Soc Microbiol
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 …
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.
American Society for Microbiology