Nucleic Acids Research Advance Access originally published online on November 7, 2006
Nucleic Acids Research 2007 35(Database issue):D169-D172; doi:10.1093/nar/gkl889
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, Database issue D169-D172
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
1 Center for Microbial Ecology, Biomedical Physical Sciences, Michigan State University East Lansing, MI 48824-4320, USA 2 Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University East Lansing, MI 48824-4320, USA
*To whom correspondence should be addressed. Tel: +1 517 353 3842; Fax: +1 517 353 8957; Email: colej{at}msu.edu
Received September 15, 2006. Accepted October 9, 2006.
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/).
![]()
CiteULike
Connotea
Del.icio.us What's this?
This article has been cited by other articles:
![]() |
C. D. Garner, D. A. Antonopoulos, B. Wagner, G. E. Duhamel, I. Keresztes, D. A. Ross, V. B. Young, and C. Altier Perturbation of the Small Intestine Microbial Ecology by Streptomycin Alters Pathology in a Salmonella enterica Serovar Typhimurium Murine Model of Infection Infect. Immun., July 1, 2009; 77(7): 2691 - 2702. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Y. Hwang, G. D. Bae, W. Yih, and B. C. Cho Marivita cryptomonadis gen. nov., sp. nov. and Marivita litorea sp. nov., of the family Rhodobacteraceae, isolated from marine habitats Int J Syst Evol Microbiol, July 1, 2009; 59(7): 1568 - 1575. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. S. Gordon, A. Valenzuela, S. M. Adams, P. W. Ramsey, J. L. Pollock, W. E. Holben, and J. E. Gannon Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil Int J Syst Evol Microbiol, July 1, 2009; 59(7): 1720 - 1726. [Abstract] [Full Text] [PDF] |
||||
![]() |
Z. Xu and B. Hao CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes Nucleic Acids Res., July 1, 2009; 37(suppl_2): W174 - W178. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. G. Barraclough, M. Hughes, N. Ashford-Hodges, and T. Fujisawa Inferring evolutionarily significant units of bacterial diversity from broad environmental surveys of single-locus data Biol Lett, June 23, 2009; 5(3): 425 - 428. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Severgnini, P. Cremonesi, C. Consolandi, G. Caredda, G. De Bellis, and B. Castiglioni ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design Nucleic Acids Res., June 16, 2009; (2009) gkp499v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. P. Davis, N. H. Youssef, and M. S. Elshahed Assessment of the Diversity, Abundance, and Ecological Distribution of Members of Candidate Division SR1 Reveals a High Level of Phylogenetic Diversity but Limited Morphotypic Diversity Appl. Envir. Microbiol., June 15, 2009; 75(12): 4139 - 4148. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. E. Escalante, J. Caballero-Mellado, L. Martinez-Aguilar, A. Rodriguez-Verdugo, A. Gonzalez-Gonzalez, J. Toribio-Jimenez, and V. Souza Pseudomonas cuatrocienegasensis sp. nov., isolated from an evaporating lagoon in the Cuatro Cienegas valley in Coahuila, Mexico Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1416 - 1420. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. I. Zhang, C. Y. Hwang, S.-H. Kang, and B. C. Cho Maribacter antarcticus sp. nov., a psychrophilic bacterium isolated from a culture of the Antarctic green alga Pyramimonas gelidicola Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1455 - 1459. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. B. Slobodkina, T. V. Kolganova, N. A. Chernyh, J. Querellou, E. A. Bonch-Osmolovskaya, and A. I. Slobodkin Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent Int J Syst Evol Microbiol, June 1, 2009; 59(6): 1508 - 1512. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. R. Vartoukian, R. M. Palmer, and W. G. Wade Diversity and Morphology of Members of the Phylum "Synergistetes" in Periodontal Health and Disease Appl. Envir. Microbiol., June 1, 2009; 75(11): 3777 - 3786. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. A. Grice, H. H. Kong, S. Conlan, C. B. Deming, J. Davis, A. C. Young, NISC Comparative Sequencing Program, G. G. Bouffard, R. W. Blakesley, P. R. Murray, et al. Topographical and Temporal Diversity of the Human Skin Microbiome Science, May 29, 2009; 324(5931): 1190 - 1192. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Tomaras, J. W. Sahl, R. L. Siegrist, and J. R. Spear Microbial Diversity of Septic Tank Effluent and a Soil Biomat Appl. Envir. Microbiol., May 15, 2009; 75(10): 3348 - 3351. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Nikolausz, A. Chatzinotas, A. Tancsics, G. Imfeld, and M. Kastner Evaluation of Single-Nucleotide Primer Extension for Detection and Typing of Phylogenetic Markers Used for Investigation of Microbial Communities Appl. Envir. Microbiol., May 1, 2009; 75(9): 2850 - 2860. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. F. Petrosino, S. Highlander, R. A. Luna, R. A. Gibbs, and J. Versalovic Metagenomic Pyrosequencing and Microbial Identification Clin. Chem., May 1, 2009; 55(5): 856 - 866. [Abstract] [Full Text] [PDF] |
||||
![]() |
P.-Y. Hong, G. C. Yap, B. W. Lee, K. Y. Chua, and W.-T. Liu Hierarchical Oligonucleotide Primer Extension as a Time- and Cost-Effective Approach for Quantitative Determination of Bifidobacterium spp. in Infant Feces Appl. Envir. Microbiol., April 15, 2009; 75(8): 2573 - 2576. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. H. Choi, C. Y. Hwang, and B. C. Cho Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater Int J Syst Evol Microbiol, April 1, 2009; 59(4): 818 - 823. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. K. Kim, S. M. Thomas, M. Ho, S. Sharma, C. I. Reich, J. A. Frank, K. M. Yeater, D. R. Biggs, N. Nakamura, R. Stumpf, et al. Heterogeneity of Vaginal Microbial Communities within Individuals J. Clin. Microbiol., April 1, 2009; 47(4): 1181 - 1189. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Gunther, M. Trutnau, S. Kleinsteuber, G. Hause, T. Bley, I. Roske, H. Harms, and S. Muller Dynamics of Polyphosphate-Accumulating Bacteria in Wastewater Treatment Plant Microbial Communities Detected via DAPI (4',6'-Diamidino-2-Phenylindole) and Tetracycline Labeling Appl. Envir. Microbiol., April 1, 2009; 75(7): 2111 - 2121. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. Nasidze, J. Li, D. Quinque, K. Tang, and M. Stoneking Global diversity in the human salivary microbiome Genome Res., April 1, 2009; 19(4): 636 - 643. [Abstract] [Full Text] [PDF] |
||||
![]() |
Z. M.-P. Lee, C. Bussema III, and T. M. Schmidt rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea Nucleic Acids Res., January 1, 2009; 37(suppl_1): D489 - D493. [Abstract] [Full Text] [PDF] |
||||
![]() |
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, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis Nucleic Acids Res., January 1, 2009; 37(suppl_1): D141 - D145. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. Luque, M. L. Riera-Alberola, A. Andujar, and J. A. G. Ochoa de Alda Intraphylum Diversity and Complex Evolution of Cyanobacterial Aminoacyl-tRNA Synthetases Mol. Biol. Evol., November 1, 2008; 25(11): 2369 - 2389. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. S. Balakirev, V. A. Pavlyuchkov, and F. J. Ayala DNA variation and symbiotic associations in phenotypically diverse sea urchin Strongylocentrotus intermedius PNAS, October 21, 2008; 105(42): 16218 - 16223. [Abstract] [Full Text] [PDF] |
||||
![]() |
Z. Huang, Y. Wu, J. Robertson, L. Feng, R. L. Malmberg, and L. Cai Fast and accurate search for non-coding RNA pseudoknot structures in genomes Bioinformatics, October 15, 2008; 24(20): 2281 - 2287. [Abstract] [Full Text] [PDF] |
||||
![]() |
Z. Liu, T. Z. DeSantis, G. L. Andersen, and R. Knight Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers Nucleic Acids Res., October 1, 2008; 36(18): e120 - e120. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Manichanh, C. E. Chapple, L. Frangeul, K. Gloux, R. Guigo, and J. Dore A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library Nucleic Acids Res., September 1, 2008; 36(16): 5180 - 5188. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Krause, N. N. Diaz, A. Goesmann, S. Kelley, T. W. Nattkemper, F. Rohwer, R. A. Edwards, and J. Stoye Phylogenetic classification of short environmental DNA fragments Nucleic Acids Res., April 1, 2008; 36(7): 2230 - 2239. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Pruesse, C. Quast, K. Knittel, B. M. Fuchs, W. Ludwig, J. Peplies, and F. O. Glockner SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Nucleic Acids Res., December 18, 2007; 35(21): 7188 - 7196. [Abstract] [Full Text] [PDF] |
||||
![]() |
C.-H. Yeang, J. F. J. Darot, H. F. Noller, and D. Haussler Detecting the Coevolution of Biosequences An Example of RNA Interaction Prediction Mol. Biol. Evol., September 1, 2007; 24(9): 2119 - 2131. [Abstract] [Full Text] [PDF] |
||||











