Nucleic Acids Research, 2003, Vol. 31, No. 1 442-443
© 2003 Oxford University Press
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA 1 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 5174324998; Fax: +1 5173538957; Email: rdpstaff{at}msu.edu
ABSTRACT
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{at}msu.edu.
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J.-M. Lim, C. O. Jeon, D.-J. Park, L.-H. Xu, C.-L. Jiang, and C.-J. Kim Paenibacillus xinjiangensis sp. nov., isolated from Xinjiang province in China. Int J Syst Evol Microbiol, November 1, 2006; 56(Pt 11): 2579 - 2582. [Abstract] [Full Text] [PDF]
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 N. Popp, M. Schlomann, and M. Mau Bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils. Microbiology, November 1, 2006; 152(Pt 11): 3291 - 3304. [Abstract] [Full Text] [PDF]
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M. D. J. Lynch and R. G. Thorn Diversity of Basidiomycetes in Michigan Agricultural Soils Appl. Envir. Microbiol., November 1, 2006; 72(11): 7050 - 7056. [Abstract] [Full Text] [PDF]
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S. Blanquart and N. Lartillot A Bayesian Compound Stochastic Process for Modeling Nonstationary and Nonhomogeneous Sequence Evolution Mol. Biol. Evol., November 1, 2006; 23(11): 2058 - 2071. [Abstract] [Full Text] [PDF]
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A. Chauhan and A. Ogram Phylogeny of Acetate-Utilizing Microorganisms in Soils along a Nutrient Gradient in the Florida Everglades. Appl. Envir. Microbiol., October 1, 2006; 72(10): 6837 - 6840. [Abstract] [Full Text] [PDF]
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M. Park, S. Lu, S. H. Ryu, B. S. Chung, W. Park, C.-J. Kim, and C. O. Jeon Flavobacterium croceum sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol, October 1, 2006; 56(Pt 10): 2443 - 2447. [Abstract] [Full Text] [PDF]
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A. Edlund and J. K. Jansson Changes in Active Bacterial Communities before and after Dredging of Highly Polluted Baltic Sea Sediments Appl. Envir. Microbiol., October 1, 2006; 72(10): 6800 - 6807. [Abstract] [Full Text] [PDF]
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K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras Appl. Envir. Microbiol., September 1, 2006; 72(9): 5734 - 5741. [Abstract] [Full Text] [PDF]
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R. Sekar, D. K. Mills, E. R. Remily, J. D. Voss, and L. L. Richardson Microbial Communities in the Surface Mucopolysaccharide Layer and the Black Band Microbial Mat of Black Band-Diseased Siderastrea siderea Appl. Envir. Microbiol., September 1, 2006; 72(9): 5963 - 5973. [Abstract] [Full Text] [PDF]
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Ch. V. Ramana, Ch. Sasikala, K. Arunasri, P. Anil Kumar, T. N. R. Srinivas, S. Shivaji, P. Gupta, J. Suling, and J. F. Imhoff Rubrivivax benzoatilyticus sp. nov., an aromatic, hydrocarbon-degrading purple betaproteobacterium. Int J Syst Evol Microbiol, September 1, 2006; 56(Pt 9): 2157 - 2164. [Abstract] [Full Text] [PDF]
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A. Blazejak, J. Kuever, C. Erseus, R. Amann, and N. Dubilier Phylogeny of 16S rRNA, Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase, and Adenosine 5'-Phosphosulfate Reductase Genes from Gamma- and Alphaproteobacterial Symbionts in Gutless Marine Worms (Oligochaeta) from Bermuda and the Bahamas Appl. Envir. Microbiol., August 1, 2006; 72(8): 5527 - 5536. [Abstract] [Full Text] [PDF]
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J. L. Macalady, E. H. Lyon, B. Koffman, L. K. Albertson, K. Meyer, S. Galdenzi, and S. Mariani Dominant Microbial Populations in Limestone-Corroding Stream Biofilms, Frasassi Cave System, Italy Appl. Envir. Microbiol., August 1, 2006; 72(8): 5596 - 5609. [Abstract] [Full Text] [PDF]
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C. Y. Hwang, D. H. Choi, and B. C. Cho Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1831 - 1836. [Abstract] [Full Text] [PDF]
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D. H. Choi and B. C. Cho Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1869 - 1873. [Abstract] [Full Text] [PDF]
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J.-C. Lee, J.-M. Lim, D.-J. Park, C. O. Jeon, W.-J. Li, and C.-J. Kim Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains L-lysine in its cell wall. Int J Syst Evol Microbiol, August 1, 2006; 56(Pt 8): 1893 - 1898. [Abstract] [Full Text] [PDF]
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 A. Busch and R. Backofen INFO-RNA--a fast approach to inverse RNA folding Bioinformatics, August 1, 2006; 22(15): 1823 - 1831. [Abstract] [Full Text] [PDF]
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T. A. Auchtung, C. D. Takacs-Vesbach, and C. M. Cavanaugh 16S rRNA Phylogenetic Investigation of the Candidate Division "Korarchaeota". Appl. Envir. Microbiol., July 1, 2006; 72(7): 5077 - 5082. [Abstract] [Full Text] [PDF]
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G. R. Noel and N. Atibalentja 'Candidatus Paenicardinium endonii', an endosymbiont of the plant-parasitic nematode Heterodera glycines (Nemata: Tylenchida), affiliated to the phylum Bacteroidetes. Int J Syst Evol Microbiol, July 1, 2006; 56(Pt 7): 1697 - 1702. [Abstract] [Full Text] [PDF]
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S. J. Green, E. Inbar, F. C. Michel Jr., Y. Hadar, and D. Minz Succession of Bacterial Communities during Early Plant Development: Transition from Seed to Root and Effect of Compost Amendment. Appl. Envir. Microbiol., June 1, 2006; 72(6): 3975 - 3983. [Abstract] [Full Text] [PDF]
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C. Y. Hwang and B. C. Cho Flectobacillus lacus sp. nov., isolated from a highly eutrophic pond in Korea Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1197 - 1201. [Abstract] [Full Text] [PDF]
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E. B. M. Denner, M. Kolari, D. Hoornstra, I. Tsitko, P. Kampfer, H.-J. Busse, and M. Salkinoja-Salonen Rubellimicrobium thermophilum gen. nov., sp. nov., a red-pigmented, moderately thermophilic bacterium isolated from coloured slime deposits in paper machines Int J Syst Evol Microbiol, June 1, 2006; 56(6): 1355 - 1362. [Abstract] [Full Text] [PDF]
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M. A. Patel, M. S. Ou, R. Harbrucker, H. C. Aldrich, M. L. Buszko, L. O. Ingram, and K. T. Shanmugam Isolation and characterization of Acid-tolerant, thermophilic bacteria for effective fermentation of biomass-derived sugars to lactic Acid. Appl. Envir. Microbiol., May 1, 2006; 72(5): 3228 - 3235. [Abstract] [Full Text] [PDF]
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S. Kleinsteuber, V. Riis, I. Fetzer, H. Harms, and S. Muller Population Dynamics within a Microbial Consortium during Growth on Diesel Fuel in Saline Environments. Appl. Envir. Microbiol., May 1, 2006; 72(5): 3531 - 3542. [Abstract] [Full Text] [PDF]
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V. Souza, L. Espinosa-Asuar, A. E. Escalante, L. E. Eguiarte, J. Farmer, L. Forney, L. Lloret, J. M. Rodriguez-Martinez, X. Soberon, R. Dirzo, et al. From the Cover: An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert PNAS, April 25, 2006; 103(17): 6565 - 6570. [Abstract] [Full Text] [PDF]
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D. R. Brown, D. L. Demcovitz, D. R. Plourde, S. M. Potter, M. E. Hunt, R. D. Jones, and D. S. Rotstein Mycoplasma iguanae sp. nov., from a green iguana (Iguana iguana) with vertebral disease. Int J Syst Evol Microbiol, April 1, 2006; 56(Pt 4): 761 - 764. [Abstract] [Full Text] [PDF]
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D. H. Choi and B. C. Cho Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. Int J Syst Evol Microbiol, April 1, 2006; 56(Pt 4): 771 - 776. [Abstract] [Full Text] [PDF]
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M. B. Leigh, P. Prouzova, M. Mackova, T. Macek, D. P. Nagle, and J. S. Fletcher Polychlorinated Biphenyl (PCB)-Degrading Bacteria Associated with Trees in a PCB-Contaminated Site Appl. Envir. Microbiol., April 1, 2006; 72(4): 2331 - 2342. [Abstract] [Full Text] [PDF]
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A. Chauhan and A. Ogram Fatty Acid-Oxidizing Consortia along a Nutrient Gradient in the Florida Everglades Appl. Envir. Microbiol., April 1, 2006; 72(4): 2400 - 2406. [Abstract] [Full Text] [PDF]
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