• Publications
  • Influence
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
TLDR
The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
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.
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 Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
TLDR
The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community and debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences.
Ribosomal Database Project: data and tools for high throughput rRNA analysis
TLDR
RDP now includes a collection of fungal large subunit rRNA genes, and most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.
Genomic insights that advance the species definition for prokaryotes.
TLDR
The average nucleotide identity of the shared genes between two strains was found to be a robust means to compare genetic relatedness among strains, and that ANI values of approximately 94% corresponded to the traditional 70% DNA-DNA reassociation standard of the current species definition.
The RDP-II (Ribosomal Database Project)
TLDR
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. (2000), continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands.
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
TLDR
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 are introduced.
A new version of the RDP (Ribosomal Database Project)
TLDR
The Ribosomal Database Project (RDP-II), previously described by Maidak et al. (1997), is now hosted by the Center for Microbial Ecology at Michigan State University and will provide more rapid updating of data, better data accuracy and increased user access.
Towards a Genome-Based Taxonomy for Prokaryotes
TLDR
The AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes, and could contribute significantly to a genome-based taxonomy for all microbial organisms.
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