The RDP-II (Ribosomal Database Project)

By B. Maidak, J. R. Cole, T. Lilburn, C. Parker, P. Saxman, Ryan J. Farris, George M. Garrity, G. Olsen, Thomas M. Schmidt, James M. Tiedje. Nucleic Acids Res., 2001

1,546 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a094ea0a295db1b4d86d504cd885fde5d3396c75

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Citations in the corpus

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities (2005, methodology): “We added the aligned sequences to a tree representing a range of phylogenetic groups from the Ribosomal Database Project II (29) by Phil Hugenholtz (15).”
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. (2002, methodology): “The CPU time and the sum-of-pairs and column scores (8) of each method are shown for the full LSU data set (72 sequences) retrieved from RDP-II (33), which includes some fragment sequences, and a subset composed of 59 sequences without fragment sequences.”
Diversity and composition of tropical soil nitrifiers across a plant diversity gradient and among land‐use types (2004, methodology): “We used the ARB software package (Ludwig & Strunk 1999) and the Ribosomal Database Project database (Maidak et al. 2001) to align the rDNA sequences in our clone library and to determine their phylogenetic affiliations.”
Utility of complete large and small subunit rRNA genes in resolving the phylogeny of the Neodermata (Platyhelminthes): implications and a review of the cercomer theory (2003, methodology): “…structure of SSU were determined with reference to appendix A in Olson & Caira (1999), and of LSU by aligning our Schistosoma mansoni sequence to Herdmania momus using the online alignment tool in RDP-II (Maidak et al., 2001) and then with reference to the models published in Degnan et al. (1990).”
Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing (2014, methodology): “The coverage of the previous and present primer sets was checked against good quality sequences (as defined based on Pintail scores by the RDP database) of greater than 1,200 bp and #1 mismatches [26] in the RDP database (Release 10) using the feature Probe Match program [27].”
probeBase: an online resource for rRNA-targeted oligonucleotide probes (2003, background): “We thank James R. Cole from RDP-II for allowing us to directly submit oligonucleotide sequences to the probe match tool of RDP-II and for giving us insight into the probe match user statistics.”