The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

By James R. Cole, Benli Chai, T. Marsh, Ryan J. Farris, Qiong Wang, S. A. Kulam, S. Chandra, Donna M. McGarrell, Thomas M. Schmidt, George M. Garrity and 1 more. Nucleic Acids Res., 2003

1,523 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/867c65a699abb0ca217a5a77b19db7043020f7bf

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Citations in the corpus

Benthic cyanobacterial bloom impacts the reefs of South Florida (Broward County, USA) (2005, methodology): “Sequences were assembled using Sequencher 4.1 (GeneCodes, Ann Arbor, MI); potential chimeric sequences were examined using Chimera Check (Cole et al. 2003).”
Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids (2006, positive): “16S rRNA gene sequences have been used extensively to analyse prokaryotic diversity in both cultures and natural environments and hence a large number of these sequences now exist (Cole et al. 2003).”
Towards a Genome-Based Taxonomy for Prokaryotes (2005, neutral): “the newer version of Bergey’s taxonomy (9).”
New Approaches for Bioaugmentation as a Remediation Technology (2004, methodology): “40 For bioaugmentation studies, the 16S rRNA gene from the added microorganism(s) can be PCR amplified and detected by gel electrophoresis.”
Picoeukaryote diversity in coastal waters of the Pacific Ocean (2006, methodology): “Probable chimeras (Wp1, 05Np2, 30Fp2), based on CHECK-CHIMERA (Cole et al. 2003) and identification by manual alignment, composed primarily of a sequence from one organism, were trimmed to remove the chimeric portion.”
Long-term orchard groundcover management systems affect soil microbial communities and apple replant disease severity (2008, methodology): “These enzymes were chosen based on their theoretical (Ribosomal Database II, Release 8.1, Cole et al. 2003), and proven (Culman et al. 2006) resolving power.”
Metagenomic Analyses: Past and Future Trends (2010, background): “(92), or Ribosomal Database Project II (RDP II) (16), provide an important and useful resource for rRNA gene-based clas-”
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features (2017, background): “Increasing evidences indicate that these ncRNAs play critical roles in numbers of important cellular processes, including transcriptional inhibition mediated by microRNAs (5), epigenetic inheritance by Piwiinteracting RNAs (6), cell-cycle regulation (7) or even acting as structural components in rib”
New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras (2006, methodology): “Using the “View by Publication” facility on the RDP’s online hierarchy browser, all libraries submitted during 2005 were identiﬁed.”