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

By Todd Z. DeSantis, Philip Hugenholtz, Neil Larsen, Mark Rojas, Eoin L. Brodie, Keith Keller, Thomas Huber, Daniel Dalevi, Ping Hu, Gary L. Andersen. Applied and Environmental Microbiology, 2006

4,718 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/41abf43dc718e271299457bce65bccfe3feeb9d6

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Citations in the corpus

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys (2011, methodology): “, 2010a), and the concatenated alignment of OTUs was filtered to remove gaps and hypervariable regions using the GG Lane mask (DeSantis et al., 2006).”
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata (2007, background): “These include (a) GreenGenes IDs (19); (b) StrainInfo IDs (20); (c) GCAT IDs (21) and (d) IMG IDs (22).”
Advancing our understanding of the human microbiome using QIIME (2013, methodology): “We recommend the GreenGenes database (DeSantis et al., 2006; McDonald, Price, et al., 2012) as the default reference data set for assigning taxonomy, although the RDP (Cole et al.”
A diversity profile of the human skin microbiota. (2008, methodology): “Of the more than 70 described bacterial divisions (DeSantis et al. 2006a), we found only six divisions associated with the skin, and only eight divisions have been associated with the gut (Eckburg et al. 2005; Ley et al. 2005).”
The ecologist's field guide to sequence‐based identification of biodiversity (2016, neutral): “1997), Greengenes (DeSantis et al. 2006), SILVA (Pruesse et al.”
probeBase—an online resource for rRNA-targeted oligonucleotide probes: new features 2007 (2006, background): “Each probe entry contains links to directly match the probe sequence against RDP-II and Greengenes, major encompassing, regularly updated 16S rRNA sequence online databases (12,13).”
Fast Statistical Alignment (2009, methodology): “16S sequences were obtained as a random slice of prokMSA from Greengenes [65] and had an average length of 1,450 nt.”
DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection (2015, methodology): “Sequenced 16S rRNA gene fragments are first clustered into different operational taxonomic units (OTUs) in 16S rRNA-based research, then each OTU is assigned to a particular taxon by comparison against known 16S rRNA databases (e.g., RDP, Greengene and SILVA [16 – 18]).”
Experimental factors affecting PCR-based estimates of microbial species richness and evenness (2010, methodology): “Overall, 97% operational taxonomic units (OTUs) were classified taxonomically by blastn comparisons against the greengenes database (DeSantis et al., 2006) using a word length of 25.”
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data (2013, methodology): “Barcoded [2] amplicon sequencing of dozens to hundreds of samples [4] is a method of phylogenetic sequencing of micro-biomes, often targeting the small subunit ribosomal RNA (16S rRNA) gene [3], for which there are also convenient tools [5] and large reference databases [6–8].”
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics (2015, positive): “16S analysis followed the same steps as 18S; however, closed reference OTUs were picked with Usearch against the Green Genes database (DeSantis et al., 2006).”
The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy (2012, background): “There are presently three databases, SILVA (20), RDP (21) and Green genes (22), offering a curated taxonomy for prokaryotic SSU rRNA sequences.”
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies (2015, methodology): “Noncoding RNAs such as tRNAs are predicted using programs like tRNAscan, 91,92 ribosomal RNA (rRNA) genes (5s, 16s, and 23s) are predicted using internally developed rRNA models for IMG/MER, and MG-RAST uses similarity to compare three known databases (SILVA, 93 Greengenes, 94 and the Ribosomal Data”