Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.
Journal:
Appl. Environ. Microbiol. 2006 JulAuthors:
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL
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 lineag
...[more]es in the Archaea and Bacteria.[less]
Mesh Headings:
Archaea, Bacteria, Databases, Nucleic Acid, Genes, rRNA, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Recombination, Genetic, Reproducibility of Results, Sequence Alignment, Software