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

Todd Z. DeSantis | Zendy; Philip Hugenholtz | Zendy; N. Larsen | Zendy; Mark Rojas | Zendy; Eoin Brodie | Zendy; Keith Keller | Zendy; Thomas Huber | Zendy; Daniel Dalevi | Zendy; Pengwei Hu | Zendy; Gary L. Andersen | Zendy

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

Author(s) -

Todd Z. DeSantis,

Philip Hugenholtz,

N. Larsen,

Mark Rojas,

Eoin Brodie,

Keith Keller,

Thomas Huber,

Daniel Dalevi,

Pengwei Hu,

Gary L. Andersen

Publication year - 2006

Publication title -

applied and environmental microbiology

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.552

H-Index - 324

eISSN - 1070-6291

pISSN - 0099-2240

DOI - 10.1128/aem.03006-05

Subject(s) - phylum , 16s ribosomal rna , biology , workbench , bacterial taxonomy , chimera (genetics) , archaea , ribosomal rna , gene , computational biology , taxonomic rank , genetics , database , data mining , ecology , computer science , taxon , visualization

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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