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

Applied and Environmental Microbiology - Tập 72 Số 7 - Trang 5069-5072 - 2006
Todd Z. DeSantis1, Philip Hugenholtz2, N. Larsen3, Mark Rojas4, Eoin Brodie1, Kenneth H. Keller5, Thomas Huber6, Daniel Dalevi7, Pengwei Hu1, Gary L. Andersen1
1Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
2Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400-404, Walnut Creek, California 94598
3Danish Genome Institute, Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
4Department of Bioinformatics, Baylor University, P.O. Box 97356, 1311 S. 5th St., Waco, Texas 76798-7356
5Department of Bioengineering, University of California, Berkeley, California 94720
6Departments of Biochemistry and Mathematics, The University of Queensland, Brisbane, Queensland 4072, Australia
7Department of Computer Science, Chalmers University of Technology, SE-412 96 Göteborg, Sweden

Tóm tắt

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 .

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Tài liệu tham khảo

10.1016/S0022-2836(05)80360-2

10.1128/AEM.71.12.7724-7736.2005

10.1093/nar/gkf450

10.1007/s00248-002-2012-1

10.1128/AEM.70.12.7161-7172.2004

10.1093/bioinformatics/btg430

10.1093/nar/gki038

10.1093/bioinformatics/btg200

Nucleic Acids Res.

10.1016/j.femsle.2005.03.016

10.1093/nar/gkg569

Felsenstein, J. 1989. PHYLIP—Phylogeny Inference Package (version 3.65). Cladistics5:164-166.

10.1128/AEM.70.2.845-849.2004

10.1101/gr.652803

10.1093/bioinformatics/bth226

10.1186/gb-2002-3-7-research0034

10.1016/j.watres.2005.05.044

10.1093/bib/5.2.150

10.1128/jb.174.1.269-278.1992

10.1016/j.femsle.2005.04.002

10.1093/nar/gkh293

10.1093/nar/29.1.173

10.1126/science.276.5313.734

10.1046/j.1472-765x.2002.01048.x

10.1128/AEM.71.3.1671-1673.2005

10.1128/MMBR.68.4.686-691.2004

10.1093/bioinformatics/bti191

10.1093/nar/25.24.4876

10.1016/S0167-7012(03)00140-4

10.1128/AEM.68.5.2535-2541.2002

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Applied and Environmental Microbiology

Tập 72 Số 7

5069-5072

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