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Methods

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

T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, G. L. Andersen
T. Z. DeSantis
1Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
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P. Hugenholtz
2Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400-404, Walnut Creek, California 94598
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N. Larsen
3Danish Genome Institute, Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
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M. Rojas
4Department of Bioinformatics, Baylor University, P.O. Box 97356, 1311 S. 5th St., Waco, Texas 76798-7356
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E. L. Brodie
1Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
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K. Keller
5Department of Bioengineering, University of California, Berkeley, California 94720
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T. Huber
6Departments of Biochemistry and Mathematics, The University of Queensland, Brisbane, Queensland 4072, Australia
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D. Dalevi
7Department of Computer Science, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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P. Hu
1Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
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G. L. Andersen
1Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
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  • For correspondence: GLAndersen@lbl.gov
DOI: 10.1128/AEM.03006-05
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    FIG. 1.

    16S rRNA gene sequencing projects that produced more than 200 full-length records. All projects were submitted to GenBank between October 2000 and February 2006. Sequences were generated from gastrointestinal (GI), soil (SO), vaginal (VG), aerosol (AR), culture collection (CC), insect (IN), water (WA), waste treatment (WT), and fecal (FC) sources as indicated on the x axis. The projects are ordered by sequence count.

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    FIG. 2.

    Phylum-level nomenclature shared by independent curators represented as a five-way Venn diagram. Yellow spheres represent the 126 phylum or candidate division names encountered in at least one of the five taxonomy systems (Pace, Hugenholtz, Ludwig, RDP, or NCBI). The numbers in parentheses are the counts for phylum or candidate division names recognized by an individual curator. Clusters of yellow spheres connected by more than one colored web symbolize names recognized by multiple curators. The image was rendered by the AutoFocus software (Aduna B.V., The Netherlands). A complete table of phylum-level nomenclature comparisons is available at http://greengenes.lbl.gov/TaxCompare .

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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, G. L. Andersen
Applied and Environmental Microbiology Jul 2006, 72 (7) 5069-5072; DOI: 10.1128/AEM.03006-05

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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, G. L. Andersen
Applied and Environmental Microbiology Jul 2006, 72 (7) 5069-5072; DOI: 10.1128/AEM.03006-05
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KEYWORDS

Databases, Nucleic Acid
Genes, rRNA
RNA, Ribosomal, 16S
Recombination, Genetic
Sequence Alignment
Software

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