The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

By James R. Cole, Qiong Wang, Erick Cardenas, Jordan A. Fish, Benli Chai, Ryan J. Farris, A. S. Kulam-Syed-Mohideen, Donna M. McGarrell, T. Marsh, George M. Garrity and 1 more. 2008

4,875 citations recorded by the source corpus.

The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks (2013, background): “and the subsequent classification of rRNA gene sequences (35,36).”
Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine (2009, positive): “The following universal 16S rRNA primers were used for the PCR reaction: 520F (5 9 -AYTGGGYDTAAAGNG-3 9 ) and 802R (5 9 - TACNVGGGTATCTAATCC-3 9 ) for the V4 region (RDP’s Pyrosequencing Pipeline: http://pyro.cme.msu.edu/pyro/help. jsp); and 986F (5 9 -CNACGCGAAGAACCTTANC-3 9 ) and 1027R (5 9 -CGACR”
Microbial Co-occurrence Relationships in the Human Microbiome (2012, background): “Sequences of both 16S windows were processed separately using mothur [71] into phylotypes using the RDP taxonomy as described in [29] and [68], with full protocols also available on the HMP DACC website (http:// hmpdacc.org/HMMCP).”
Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host (2014, positive): “bosomal Database Project (RDP) website (34) and were trimmed to rep-”
Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis (2012, neutral): “0, training set 4 (Cole et al. 2009).”
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance (2012, methodology): “Bacterial reference phylogeny with genomic 16S copy number indicated with black bars (bar length proportional to genomic 16S copy number) and taxonomic order (determined using RDP Taxonomic Classifier [43]) indicated with color shading of branches.”
Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing (2011, methodology): “For amplifying the V4 region, we used modifications of the primers described on the RDP (Cole et al., 2009) Pyrosequencing website (http://rdp.cme. msu.edu/).”
Microbes inside—from diversity to function: the case of Akkermansia (2012, background): “Current public sequence databases contain over a million full-length 16S rRNA sequences spanning a broad phylogenetic range (Cole et al., 2009).”
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes (2013, background): “While 16S databases, and thus phylogenies, include millions of sequences covering a substantial fraction of all microbes 11,12 , relying on any single gene lacks phylogenetic resolution at evolutionarily short time scales, preventing differentiation of closely-related organisms 13 , and mutations…”