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

@article{Cole2007TheRD,
  title={The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data},
  author={James R. Cole and Benli Chai and Ryan J. Farris and Qiong Wang and A. S. Kulam-Syed-Mohideen and Donna M. McGarrell and A. M. Bandela and Erick Cardenas and George M. Garrity and James M. Tiedje},
  journal={Nucleic Acids Research},
  year={2007},
  volume={35},
  pages={D169 - D172}
}
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… 

Tables from this paper

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
TLDR
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, and a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data.
TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels
TLDR
The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil.
rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea
TLDR
The Ribosomal RNA Database is expanded to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms, and the revamped database computes average gene copy numbers for any collection of entries selected.
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
TLDR
The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
rrn DB : documenting the number of rRNA and tRNA genes in bacteria and archaea
TLDR
The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial communities, and is redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms.
An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)
TLDR
This work describes here their fully-automated ss-rRNA taxonomy and alignment pipeline (STAP), which generates both high-quality multiple sequence alignments and phylogenetic trees, and thus can be used for multiple purposes including phylogenetically-based taxonomic assignments and analysis of species diversity in environmental samples.
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
TLDR
SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains.
A renaissance for the pioneering 16S rRNA gene.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 24 REFERENCES
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
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
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
TLDR
This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at the Comparative RNA Web (CRW) Site.
ARB: a software environment for sequence data.
TLDR
The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface.
At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies
TLDR
The method is implemented as a program with a simple-to-use graphic user interface that is capable of running on a range of computer platforms and concludes that, as a conservative estimate, 1 in every 20 public database records is likely to be corrupt.
Quantitative Comparisons of 16S rRNA Gene Sequence Libraries from Environmental Samples
TLDR
This method successfully distinguished rRNA gene sequence libraries from soil and bioreactors and correctly failed to find differences between libraries of the same composition.
At least one in twenty 16 S rRNA sequence records currently held in public 1 repositories estimated to contain substantial anomalies
TLDR
A new method for detecting chimeras and other anomalies within 16S rRNA sequence 2 records is presented and it is concluded that, as a conservative estimate, one in every twenty public database records is likely to be corrupt.
Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness
TLDR
A computer program, DOTUR, is developed, which assigns sequences to OTUs by using either the furthest, average, or nearest neighbor algorithm for each distance level, which addresses the challenge of assigning sequences to operational taxonomic units (OTUs) based on the genetic distances between sequences.
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
TLDR
A new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences, which is based on version 3.3 of Felsenstein's dnaml program and significantly improve performance and reduce memory usage, making it feasible to construct even very large trees.
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TLDR
An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Small Subunit Ribosomal RNA Modeling Using Stochastic Context-Free Grammars
TLDR
A model based on stochastic context-free grammars (SCFGs) that can construct small subunit ribosomal RNA (SSU rRNA) multiple alignments of quality close to hand edited ones and outperforms several other methods is introduced.
...
1
2
3
...