The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

By James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, S. A. Kulam, Donna M. McGarrell, George M. Garrity, James M. Tiedje. Nucleic Acids Res., 2004

1,578 citations recorded by the source corpus.

The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is rdpstaff@msu.edu.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

Towards the human intestinal microbiota phylogenetic core. (2009, background): “Hence revisited, the human GI tract microbiota appeared dominated by very few phyla when compared with other complex ecosystems such as soils and oceans (Cole et al., 2005), but nonetheless highly diverse and complex at the level of ‘phylotypes’.”
FunGene: the functional gene pipeline and repository (2013, background): “Probe Match (Myers, 1999; Cole et al., 2005) performs a search against the selected nucleotide sequences (subjects) for matches to the entered oligonucleotide sequence (query).”
Early marine bacterial biofilm on a copper-based antifouling paint (2013, methodology): “The clone sequences were further checked for chimeric artifacts using the CHECK-CHIMERA tool available in the Ribosomal Database Project (RDP) (Cole et al., 2005) and Pintail (Ashelford et al.”
Defining the Normal Bacterial Flora of the Oral Cavity (2005, positive): “Chimeric sequences were identified by using the Chimera Check program in the Ribosomal Database Project, by treeing analysis, or by base signature analysis.”
A deep learning approach to pattern recognition for short DNA sequences (2018, background): “8,9,31,36 11 Despite the recent increase in successful applications of deep learning to genomics, 46-48 to our knowledge no previous work demonstrates that DNNs can classify genomic sequencing data of realistic scales at fine taxonomic resolution, or provides an in-depth comparison to existing…”
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB (2006, methodology): “Taxonomy proposed by independent curators, including the NCBI, the Ribosomal Database Project (RDP) (Bergey’s) (7), Wolfgang Ludwig (21), Phil Hugenholtz (16), and Norman Pace (23), is tracked to promote user awareness of several estimations of phylogenetic descent, allowing a balanced approach to n”
A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales (2009, methodology): “Degenerate 16S rDNA PCR primers that exclude cyanobacterial and/or chloroplast-derived DNA from amplification (Table 1) were designed using 16S sequences from plastids (of both algae and higher plants) and over one hundred sequences (see Table S1 in the supplemental material) representing a wide div”
Phylogenetic diversity of Fe(III)-reducing microorganisms in rice paddy soil: enrichment cultures with different short-chain fatty acids as electron donors (2011, methodology): “Sequences were phylogenetically identified using RDP-II Classifier and Sequence Match (Cole et al. 2005) in combination with NCBI BLASTN search program.”
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale (2009, methodology): “The taxonomic identity of each phylotype was determined using RDPII taxonomy ( 9 ).”
The Mucin Degrader Akkermansia muciniphila Is an Abundant Resident of the Human Intestinal Tract (2007, background): “Match function (4), and a similarity search sequence of the”
Examining the global distribution of dominant archaeal populations in soil (2011, methodology): “Phylotypes were assigned an identity based on comparisons with sequences in the Ribosomal Database Project (Cole et al., 2005).”
A review of methods and databases for metagenomic classification and assembly (2019, background): “A major advantage of rRNA analysis is that databases such as Greengenes [10], RDP [11] and SILVA [12] contain genes from millions of species, making them far more comprehensive than genome databases, which contain tens of thousands of species.”
Microbial Dysbiosis in Colorectal Cancer (CRC) Patients (2011, methodology): “The trimmed sequences were assigned to taxa using the default settings of the Classifier software [32] to obtain a rapid classification of the bacterial genus.”