Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB-Reference-Cited by-同舟云学术

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

Published:2006-07 Issue:7 Volume:72 Page:5069-5072
ISSN:0099-2240
Container-title:Applied and Environmental Microbiology
language:en
Short-container-title:Appl Environ Microbiol

Author:

DeSantis T. Z.¹,Hugenholtz P.²,Larsen N.³,Rojas M.⁴,Brodie E. L.¹,Keller K.⁵,Huber T.⁶,Dalevi D.⁷,Hu P.¹,Andersen G. L.¹

Affiliation:

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

Abstract

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 .

Publisher

American Society for Microbiology

Subject

Ecology,Applied Microbiology and Biotechnology,Food Science,Biotechnology

Link

https://journals.asm.org/doi/pdf/10.1128/AEM.03006-05

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