Nucleic Acids Research, 2005, Vol. 33, Database issue D294-D296
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
1 Center for Microbial Ecology and 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: +1 517 432 4998; Fax: +1 517 353 8957; Email: rdpstaff{at}msu.edu
Received September 14, 2004; Revised and Accepted September 24, 2004
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{at}msu.edu.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
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|
|
|
|
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|
|
|
|
|
|
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|
|
|
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|
|
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|
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|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
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|
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|
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|
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|
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|
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|
|
|
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, and J. M. Tiedje The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data Nucleic Acids Res., January 12, 2007; 35(suppl_1): D169 - D172. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Li, Y. Ge, D. Saxena, and P. W. Caufield Genetic Profiling of the Oral Microbiota Associated with Severe Early-Childhood Caries J. Clin. Microbiol., January 1, 2007; 45(1): 81 - 87. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Anderson and M. G. Haygood {alpha}-Proteobacterial Symbionts of Marine Bryozoans in the Genus Watersipora Appl. Envir. Microbiol., January 1, 2007; 73(1): 303 - 311. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. L. Marco, R. S. Bongers, W. M. de Vos, and M. Kleerebezem Spatial and Temporal Expression of Lactobacillus plantarum Genes in the Gastrointestinal Tracts of Mice Appl. Envir. Microbiol., January 1, 2007; 73(1): 124 - 132. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Winter, T. Hein, G. Kavka, R. L. Mach, and A. H. Farnleitner Longitudinal Changes in the Bacterial Community Composition of the Danube River: a Whole-River Approach Appl. Envir. Microbiol., January 1, 2007; 73(2): 421 - 431. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. McGarvey, W. G. Miller, R. Zhang, Y. Ma, and F. Mitloehner Bacterial Population Dynamics in Dairy Waste during Aerobic and Anaerobic Treatment and Subsequent Storage Appl. Envir. Microbiol., January 1, 2007; 73(1): 193 - 202. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. M. Vickerman, K. A. Brossard, D. B. Funk, A. M. Jesionowski, and S. R. Gill Phylogenetic analysis of bacterial and archaeal species in symptomatic and asymptomatic endodontic infections J. Med. Microbiol., January 1, 2007; 56(1): 110 - 118. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Letunic and P. Bork Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation Bioinformatics, January 1, 2007; 23(1): 127 - 128. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Chalmin, F. d'Orlye, L. Zinger, L. Charlet, R. A. Geremia, G. Orial, M. Menu, D. Baffier, and I. Reiche Biotic versus abiotic calcite formation on prehistoric cave paintings: the Arcy-sur-Cure 'Grande Grotte' (Yonne, France) case Geological Society, London, Special Publications, January 1, 2007; 279(1): 185 - 197. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. M. Heimesaat, S. Bereswill, A. Fischer, D. Fuchs, D. Struck, J. Niebergall, H.-K. Jahn, I. R. Dunay, A. Moter, D. M. Gescher, et al. Gram-Negative Bacteria Aggravate Murine Small Intestinal Th1-Type Immunopathology following Oral Infection with Toxoplasma gondii J. Immunol., December 15, 2006; 177(12): 8785 - 8795. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Matsuo, A. Katsuta, S. Matsuda, Y. Shizuri, A. Yokota, and H. Kasai Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov. Int J Syst Evol Microbiol, December 1, 2006; 56(12): 2837 - 2842. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. P. Drees, J. W. Neilson, J. L. Betancourt, J. Quade, D. A. Henderson, B. M. Pryor, and R. M. Maier Bacterial Community Structure in the Hyperarid Core of the Atacama Desert, Chile Appl. Envir. Microbiol., December 1, 2006; 72(12): 7902 - 7908. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Waldeck, G. Daum, B. Bisping, and F. Meinhardt Isolation and Molecular Characterization of Chitinase-Deficient Bacillus licheniformis Strains Capable of Deproteinization of Shrimp Shell Waste To Obtain Highly Viscous Chitin Appl. Envir. Microbiol., December 1, 2006; 72(12): 7879 - 7885. [Abstract] [Full Text] [PDF]
|
|
|
|
|
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M. Hartmann and F. Widmer Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices Appl. Envir. Microbiol., December 1, 2006; 72(12): 7804 - 7812. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Dinoto, T. M. Marques, K. Sakamoto, S. Fukiya, J. Watanabe, S. Ito, and A. Yokota Population Dynamics of Bifidobacterium Species in Human Feces during Raffinose Administration Monitored by Fluorescence In Situ Hybridization-Flow Cytometry Appl. Envir. Microbiol., December 1, 2006; 72(12): 7739 - 7747. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Sheneman, J. Evans, and J. A. Foster Clearcut: a fast implementation of relaxed neighbor joining Bioinformatics, November 15, 2006; 22(22): 2823 - 2824. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Canchaya, M. J. Claesson, G. F. Fitzgerald, D. van Sinderen, and P. W. O'Toole Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology, November 1, 2006; 152(Pt 11): 3185 - 3196. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Piccini, D. Conde, C. Alonso, R. Sommaruga, and J. Pernthaler Blooms of single bacterial species in a coastal lagoon of the southwestern atlantic ocean. Appl. Envir. Microbiol., October 1, 2006; 72(10): 6560 - 6568. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. R. Penton, A. H. Devol, and J. M. Tiedje Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments. Appl. Envir. Microbiol., October 1, 2006; 72(10): 6829 - 6832. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. E. Morey, R. L. Galloway, S. L. Bragg, A. G. Steigerwalt, L. W. Mayer, and P. N. Levett Species-Specific Identification of Leptospiraceae by 16S rRNA Gene Sequencing. J. Clin. Microbiol., October 1, 2006; 44(10): 3510 - 3516. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Mateos, S. J. Castrezana, B. J. Nankivell, A. M. Estes, T. A. Markow, and N. A. Moran Heritable Endosymbionts of Drosophila Genetics, September 1, 2006; 174(1): 363 - 376. [Abstract] [Full Text] [PDF]
|
|
|
|
|
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S. N. Jarman Cleaver: software for identifying taxon specific restriction endonuclease recognition sites Bioinformatics, September 1, 2006; 22(17): 2160 - 2161. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. L. Sogin, H. G. Morrison, J. A. Huber, D. M. Welch, S. M. Huse, P. R. Neal, J. M. Arrieta, and G. J. Herndl Microbial diversity in the deep sea and the underexplored "rare biosphere" PNAS, August 8, 2006; 103(32): 12115 - 12120. [Abstract] [Full Text] [PDF]
|
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S. Vainberg, K. McClay, H. Masuda, D. Root, C. Condee, G. J. Zylstra, and R. J. Steffan Biodegradation of Ether Pollutants by Pseudonocardia sp. Strain ENV478 Appl. Envir. Microbiol., August 1, 2006; 72(8): 5218 - 5224. [Abstract] [Full Text] [PDF]
|
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