The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data

By James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, A. S. Kulam-Syed-Mohideen, Donna M. McGarrell, A. M. Bandela, Erick Cardenas, George M. Garrity, James M. Tiedje. Nucleic Acids Res., 2006

1,208 citations recorded by the source corpus.

Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own data in context with the RDP's data. In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website ().

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3ca66c49d97654512cac710448eea1d134b226cf

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Citations in the corpus

Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. (2010, methodology): “Their specificity was checked with the ProbeMatch function of the Ribosome Database Project II (Cole et al., 2007).”
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools (2012, background): “In addition to the tag ‘(T)’ used by EMBL-Bank to mark a sequence as type strain, the following tags are used by SILVA: . the label ‘e[G]’ is added if an entry is part of the list of genomes offered by the EMBL-Bank, . the label ‘l[T]’ is added if the entry is part of the type strain datasets of ‘Th”
Dysbiosis Contributes to Arthritis Development via Activation of Autoreactive T Cells in the Intestine (2016, background): “2 (21) with the SILVA 111 database (22).”
DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences (2011, background): “For instance, the Ribosomal Database Project (RDP) (4) is a major repository of bacterial and archaeal 16S rRNA sequences and offers tools for browsing, classification, probe checking, and sequence matching, among others.”
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis (2008, background): “These improvements have been extended to the my RDP user-account system described in our last update (1).”
Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use (2008, methodology): “, 2005) and a curated 16S database derived from high quality 16S sequences obtained from RDPII database (Cole et al., 2007).”
Identifying and Characterizing Bacteria in an Era of Genomics and Proteomics (2008, neutral): “Two examples of databases that provide excellent analysis for identification based on 16S rRNA gene sequence analysis are the Ribosomal Database Project (Cole et al. 2007) and greengenes (DeSantis et al. 2006).”
Monitoring Bacterial Community of Human Gut Microbiota Reveals an Increase in Lactobacillus in Obese Patients and Methanogens in Anorexic Patients (2009, methodology): “smithii systems were assessed in silico using the ribosomal RDP-II database [17].”
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers (2008, methodology): “In this study, we compare several methods: BLAST (16), the online Greengenes (17) and RDP (18) classifiers, and two treebased methods.”
A Bioinformatician's Guide to Metagenomics (2008, background): “The smallsubunit rRNA (16S rRNA) gene is usually the marker gene of choice for bacterial and archaeal communities owing to its widespread use and consequent large reference database (25, 34).”
Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome (2010, neutral): “7 [42].”