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Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

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.

Pubmed ID: 16820507

Authors

  • DeSantis TZ
  • Hugenholtz P
  • Larsen N
  • Rojas M
  • Brodie EL
  • Keller K
  • Huber T
  • Dalevi D
  • Hu P
  • Andersen GL

Journal

Applied and environmental microbiology

Publication Data

July 5, 2006

Associated Grants

None

Mesh Terms

  • Archaea
  • Bacteria
  • Databases, Nucleic Acid
  • Genes, rRNA
  • Polymerase Chain Reaction
  • RNA, Ribosomal, 16S
  • Recombination, Genetic
  • Reproducibility of Results
  • Sequence Alignment
  • Software