Database Commons

a catalog of biological databases

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Database information

RDP (Ribosomal Database Project)

General information

Description: 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.
Year founded: 1991
Last update: 2016-09-30
Version: v11.4
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States
Data type:
RNA
Data object:
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: Michigan State University
Address: East Lansing, MI 48824, USA
City: East Lansing
Province/State: MI
Country/Region: United States
Contact name (PI/Team): James R. Cole
Contact email (PI/Helpdesk): colej@msu.edu

Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2018-06-07]
Lin Xia [2016-04-01]
Zhang Zhang [2016-01-18]
Lin Xia [2015-06-26]
Jian SA [2015-06-26]

Ranking

All databases:
31/4494 (99.332%)
Gene genome and annotation:
20/1197 (98.413%)
31
Total Rank
7,782
Citations
277.929
z-index

Community reviews

Not Rated
Data quality & quantity:
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Word cloud

Publications

24288368
Ribosomal Database Project: data and tools for high throughput rRNA analysis. [PMID: 24288368]
James R Cole, Qiong Wang, Jordan A Fish, Benli Chai, Donna M McGarrell, Yanni Sun, C Titus Brown, Andrea Porras-Alfaro, Cheryl R Kuske, James M Tiedje

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.

Nucleic Acids Res. 2014:42(Database issue) | 868 Citations (from Europe PMC, 2019-12-07)
19004872
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. [PMID: 19004872]
J R Cole, Q Wang, E Cardenas, J Fish, B Chai, R J Farris, A S Kulam-Syed-Mohideen, D M McGarrell, T Marsh, G M Garrity, J M Tiedje

The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. 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. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.

Nucleic Acids Res. 2009:37(Database issue) | 2186 Citations (from Europe PMC, 2019-12-07)
17090583
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. [PMID: 17090583]
J R Cole, B Chai, R J Farris, Q Wang, A S Kulam-Syed-Mohideen, D M McGarrell, A M Bandela, E Cardenas, G M Garrity, J M Tiedje

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 (http://rdp.cme.msu.edu/).

Nucleic Acids Res. 2007:35(Database issue) | 544 Citations (from Europe PMC, 2019-12-07)
15608200
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. [PMID: 15608200]
J R Cole, B Chai, R J Farris, Q Wang, S A Kulam, D M McGarrell, G M Garrity, J M Tiedje

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 framework for these data. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101,632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is rdpstaff@msu.edu.

Nucleic Acids Res. 2005:33(Database issue) | 666 Citations (from Europe PMC, 2019-12-07)
12520046
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. [PMID: 12520046]
J R Cole, B Chai, T L Marsh, R J Farris, Q Wang, S A Kulam, S Chandra, D M McGarrell, T M Schmidt, G M Garrity, J M Tiedje, null null

The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.

Nucleic Acids Res. 2003:31(1) | 752 Citations (from Europe PMC, 2019-12-07)
11125082
The RDP-II (Ribosomal Database Project). [PMID: 11125082]
B L Maidak, J R Cole, T G Lilburn, C T Parker, P R Saxman, R J Farris, G M Garrity, G J Olsen, T M Schmidt, J M Tiedje

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.

Nucleic Acids Res. 2001:29(1) | 750 Citations (from Europe PMC, 2019-12-07)
10592216
The RDP (Ribosomal Database Project) continues. [PMID: 10592216]
B L Maidak, J R Cole, T G Lilburn, C T Parker, P R Saxman, J M Stredwick, G M Garrity, B Li, G J Olsen, S Pramanik, T M Schmidt, J M Tiedje

The Ribosomal Database Project (RDP-II), previously described by Maidak et al., continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10 700 small subunit rRNA sequences. More than 850 type strain sequences were identified and added to the prokaryotic alignment, bringing the total number of type sequences to 3324 representing 2460 different species. Availability of an RDP-II mirror site in Japan is also near completion. RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/ ). Analysis services include rRNA probe checking, approx-i-mate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments.

Nucleic Acids Res. 2000:28(1) | 260 Citations (from Europe PMC, 2019-12-07)
9847171
A new version of the RDP (Ribosomal Database Project). [PMID: 9847171]
B L Maidak, J R Cole, C T Parker, G M Garrity, N Larsen, B Li, T G Lilburn, M J McCaughey, G J Olsen, R Overbeek, S Pramanik, T M Schmidt, J M Tiedje, C R Woese

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.

Nucleic Acids Res. 1999:27(1) | 478 Citations (from Europe PMC, 2019-12-07)
9016515
The RDP (Ribosomal Database Project). [PMID: 9016515]
B L Maidak, G J Olsen, N Larsen, R Overbeek, M J McCaughey, C R Woese

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous FTP (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and WWW (http://rdpwww.life.uiuc.edu/ ). The electronic mail and WWW servers provide ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree.

Nucleic Acids Res. 1997:25(1) | 382 Citations (from Europe PMC, 2019-12-07)
8594608
The Ribosomal Database Project (RDP). [PMID: 8594608]
B L Maidak, G J Olsen, N Larsen, R Overbeek, M J McCaughey, C R Woese

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and World Wide Web (WWW)(http://rdpwww.life.uiuc.edu/). The electronic mail and WWW servers provide ribosomal probe checking, screening for possible chimeric rRNA sequences, automated alignment and approximate phylogenetic placement of user-submitted sequences on an existing phylogenetic tree.

Nucleic Acids Res. 1996:24(1) | 186 Citations (from Europe PMC, 2019-12-07)
7524021
The Ribosomal Database Project. [PMID: 7524021]
B L Maidak, N Larsen, M J McCaughey, R Overbeek, G J Olsen, K Fogel, J Blandy, C R Woese

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services, and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server/rdp.life.uiuc.edu) and gopher (rdpgopher.life.uiuc.edu). The electronic mail server also provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for chimeric nature of newly sequenced rRNAs, and automated alignment.

Nucleic Acids Res. 1994:22(17) | 291 Citations (from Europe PMC, 2019-12-07)
8332524
The ribosomal database project. [PMID: 8332524]
N Larsen, G J Olsen, B L Maidak, M J McCaughey, R Overbeek, T J Macke, T L Marsh, C R Woese

The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and displaying alignments and trees. The data are available via ftp and electronic mail. Certain analytic services are also provided by the electronic mail server.

Nucleic Acids Res. 1993:21(13) | 258 Citations (from Europe PMC, 2019-12-07)
1598241
The Ribosomal Database Project. [PMID: 1598241]
G J Olsen, R Overbeek, N Larsen, T L Marsh, M J McCaughey, M A Maciukenas, W M Kuan, T J Macke, Y Xing, C R Woese

The Ribosomal Database Project (RDP) complies ribosomal sequences and related data, and redistributes them in aligned and phylogenetically ordered form to its user community. It also offers various software packages for handling, analyzing and displaying sequences. In addition, the RDP offers (or will offer) certain analytic services. At present the project is in an intermediate stage of development.

Nucleic Acids Res. 1992:20 Suppl() | 101 Citations (from Europe PMC, 2019-12-07)
2041798
The ribosomal RNA database project. [PMID: 2041798]
G J Olsen, N Larsen, C R Woese
Nucleic Acids Res. 1991:19 Suppl() | 60 Citations (from Europe PMC, 2019-12-07)