Ribosomal Database Project: Data and tools for high throughput rRNA analysis

James R. Cole, Qiong Wang, Jordan A. Fish, Benli Chai, Donna M. McGarrell, Yanni Sun, Charles Brown, Andrea Porras-Alfaro, Cheryl R. Kuske, James M. Tiedje

Research output: Contribution to journalArticle

1327 Citations (Scopus)

Abstract

Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, 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.

Original languageEnglish (US)
JournalNucleic Acids Research
Volume42
Issue numberD1
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

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rRNA Genes
Databases
Environmental Microbiology
Research Personnel
Ecology
Nucleic Acids
Technology
Health
Research
Population

ASJC Scopus subject areas

  • Genetics

Cite this

Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., ... Tiedje, J. M. (2014). Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Research, 42(D1). https://doi.org/10.1093/nar/gkt1244

Ribosomal Database Project : Data and tools for high throughput rRNA analysis. / Cole, James R.; Wang, Qiong; Fish, Jordan A.; Chai, Benli; McGarrell, Donna M.; Sun, Yanni; Brown, Charles; Porras-Alfaro, Andrea; Kuske, Cheryl R.; Tiedje, James M.

In: Nucleic Acids Research, Vol. 42, No. D1, 01.01.2014.

Research output: Contribution to journalArticle

Cole, JR, Wang, Q, Fish, JA, Chai, B, McGarrell, DM, Sun, Y, Brown, C, Porras-Alfaro, A, Kuske, CR & Tiedje, JM 2014, 'Ribosomal Database Project: Data and tools for high throughput rRNA analysis', Nucleic Acids Research, vol. 42, no. D1. https://doi.org/10.1093/nar/gkt1244
Cole, James R. ; Wang, Qiong ; Fish, Jordan A. ; Chai, Benli ; McGarrell, Donna M. ; Sun, Yanni ; Brown, Charles ; Porras-Alfaro, Andrea ; Kuske, Cheryl R. ; Tiedje, James M. / Ribosomal Database Project : Data and tools for high throughput rRNA analysis. In: Nucleic Acids Research. 2014 ; Vol. 42, No. D1.
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