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

Journal Article · Mon Apr 10 00:00:00 EDT 2006 · Applied and Environmental Microbiology

DOI:https://doi.org/10.1128/AEM.03006-05· OSTI ID:898565

DeSantis, Todd Z; Hugenholtz, Philip; Larsen, Neils; Rojas, Mark; Brodie, Eoin L; Keller, Keith; Huber, Thomas; Dalevi, Daniel; Hu, Ping; Andersen, Gary L

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.

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Director. Office of Science. Office of AdvancedScientific Computing Research. Office of Biological and EnvironmentalResearch. Genomics GTL Program, National and Accelerated BioremediationResearch Program; Department of Homeland Security GrantHSSCHQ04X00037
• DOE Contract Number: DE-AC02-05CH11231
• OSTI ID: 898565
• Report Number(s): LBNL-59764; AEMIDF; R&D Project: G4W064; BnR: 400904010; TRN: US200706%%117
• Journal Information: Applied and Environmental Microbiology, Vol. 72, Issue 7; Related Information: Journal Publication Date: July 2006; ISSN 0099-2240
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
BACTERIA
CHIMERAS
CLASSIFICATION
GENES
16S rRNA bacteria archaea taxonomy chimera