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

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

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.

Related collections

Author and article information

Journal

Title: Applied and Environmental Microbiology

Abbreviated Title: AEM

Publisher: American Society for Microbiology

ISSN (Print): 0099-2240

ISSN (Electronic): 1098-5336

Publication date Created: July 2006

Publication date (Print): July 2006

Volume: 72

Issue: 7

Pages: 5069-5072

Affiliations

[1 ] Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720

[2 ] Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400-404, Walnut Creek, California 94598

[3 ] Danish Genome Institute, Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark

[4 ] Department of Bioinformatics, Baylor University, P.O. Box 97356, 1311 S. 5th St., Waco, Texas 76798-7356

[5 ] Department of Bioengineering, University of California, Berkeley, California 94720

[6 ] Departments of Biochemistry and Mathematics, The University of Queensland, Brisbane, Queensland 4072, Australia

[7 ] Department of Computer Science, Chalmers University of Technology, SE-412 96 Göteborg, Sweden

Article

DOI: 10.1128/AEM.03006-05

PMC ID: 1489311

PubMed ID: 16820507

SO-VID: a7caa567-3e65-41ce-b008-966bd11dc1b5

History

Data availability:

Comments

Comment on this article

scite_

Cited by 4,394

See all cited by