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RDP's License Agreement:


RDP services' data representation and analysis results obtained through The Ribosomal Database Project are freely available under the Creative Commons Attribution-ShareAlike 3.0 Unported License.
Please visit http://creativecommons.org/licenses/by-sa/3.0/ to view the terms of this license. Creative Commons License


How to cite services from this site


If you download data or use software available from RDP, please cite us in the following way:
Cole, J. R., Q. Wang, J. A. Fish, B. Chai, D. M. McGarrell, Y. Sun, C. T. Brown, A. Porras-Alfaro, C. R. Kuske, and J. M. Tiedje. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucl. Acids Res. 42(Database issue):D633-D642; doi: 10.1093/nar/gkt1244 [PMID: 24288368]

If you use RDP's Classifier, please cite:
Wang, Q, G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol. 73(16):5261-5267; doi: 10.1128/AEM.00062-07 [PMID: 17586664]

If you use RDP's FrameBot, please cite:
Wang, Q., J. F. Quensen III, J. A. Fish, T.-K. Lee, Y. Sun, J. M. Tiedje, J. R. Cole. 2013. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. mBio 4:e00592-13; doi: 10.1128/mBio.00592-13

If you use RDP's FunGene, please cite:
Fish, J. A., B. Chai, Q. Wang, Y. Sun, C. T. Brown, J. M. Tiedje, and J. R. Cole. 2013. FunGene: the Functional Gene Pipeline and Repository. Front. Microbiol. 4:291; doi: 10.3389/fmicb.2013.00291

If you use RDP's Xander, please cite:
Wang, Q., J. A. Fish, M. Gilman, Y. Sun, C. T. Brown, J. M. Tiedje, and J. R. Cole. 2015. Xander: employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome 3:32; doi: 10.1186/s40168-015-0093-6


For more details on using RDP tools, please read Chapter 36:
Cole J.R., Q. Wang, B. Chai and J.M. Tiedje. 2011. The Ribosomal Database Project: sequences and software for high-throughput rRNA analysis. In F.J. de Bruijn (ed), Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches, J. Wiley & Sons, Inc., Hoboken, NJ.



Previous RDP Publications


Cole, J. R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity, and J. M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37 (Database issue): D141-145; doi: 10.1093/nar/gkn879 [PMID: 19004872]

Cole, J. R., B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, G. M. Garrity, and J. M. Tiedje. 2007. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35 (Database issue): D169-D172; doi: 10.1093/nar/gkl889 [PMID: 17090583]

Cole, J. R., B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity, and J. M. Tiedje. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33 (Database Issue):D294-D296; doi: 10.1093/nar/gki038 [PMID: 15608200]

Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31(1):442-443; doi: 1a0.1093/nr/gkg039 [PMID: 12520046]

Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, Jr., P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29(1):173-174; doi: 10.1093/nar/29.1.173 [PMID: 11125082]

Maidak, B. L., J. R. Cole, C. T. Parker, Jr., 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, and C. R. Woese. 2000. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28(1):173-174; doi: 10.1093/nar/28.1.173 [PMID: 10592216]

Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27(1):171-173; doi: 10.1093/nar/27.1.171 [PMID: 9847171]

Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25(1):109-111; doi: 10.1093/nar/25.1.109 [PMID: 9016515]

Maidak, B. L., N. Larsen, M. J. McCaughey, R. Overbeek, G. J. Olsen, K. Fogel, J. Blandy, and C. R. Woese. 1996. The Ribosomal Database Project (RDP). Nucleic Acids Res. 24(1):82-85; doi: 10.1093/nar/24.1.82 [PMID: 8594608]

Maidak, B. L., N. Larsen, M. J. McCaughey, R. Overbeek, G. J. Olsen, K. Fogel, J. Blandy, and C. R. Woese. 1994. The Ribosomal Database Project. Nucleic Acids Res. 22(17):3485-3487; doi: 10.1093/nar/22.17.3485 [PMID: 7524021]

Larsen, N., G. J. Olsen, B. L. Maidak, M. J. McCaughey, R. Overbeek, T. J. Macke, T. L. Marsh, and C. R. Woese. 1993. The ribosomal database project. Nucleic Acids Res. 21(13):3021-3023; doi: 10.1093/nar/21.13.3021 [PMID: 8332524]

Olsen, G. J., R. Overbeek, N. Larsen, T. L. Marsh, M. J. McCaughey, M. A. Maciukenas, W. M. Kuan, T. J. Macke, Y. Xing, and C. R. Woese. 1992. The Ribosomal Database Project. Nucleic Acids Res. 20 Suppl:2199-2200; doi: 10.1093/nar/20.suppl.2199 [PMID: 1598241]

 

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