Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
Todd Z. DeSantisCenter for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720Philip HugenholtzMicrobial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400-404, Walnut Creek, California 94598N. LarsenDanish Genome Institute, Gustav Wieds vej 10 C, DK-8000 Aarhus C, DenmarkMark RojasDepartment of Bioinformatics, Baylor University, P.O. Box 97356, 1311 S. 5th St., Waco, Texas 76798-7356Eoin BrodieCenter for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720Keith KellerDepartment of Bioengineering, University of California, Berkeley, California 94720Thomas HuberDepartments of Biochemistry and Mathematics, The University of Queensland, Brisbane, Queensland 4072, AustraliaDaniel DaleviDepartment of Computer Science, Chalmers University of Technology, SE-412 96 Göteborg, SwedenPengwei HuCenter for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720Gary L. AndersenCenter for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
2006en
ABI
Аннотация
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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