Nucleic Acids Research, Vol 25, Issue 1 109-111, Copyright © 1997 by Oxford University Press
BL Maidak, GJ Olsen, N Larsen, R Overbeek, MJ McCaughey and CR 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.
ARTICLES
The RDP (Ribosomal Database Project)
Department of Microbiology, University of Illinois, B103 C&LSL, 601 South Goodwin Avenue, Urbana, IL 61801, USA. b-maidak@uiuc.edu
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K. Daly, R. J. Sharp, and A. J. McCarthy Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria Microbiology, July 1, 2000; 146(7): 1693 - 1705. [Abstract] [Full Text]
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D. W. Oldach, C. F. Delwiche, K. S. Jakobsen, T. Tengs, E. G. Brown, J. W. Kempton, E. F. Schaefer, H. A. Bowers, H. B. Glasgow Jr., J. M. Burkholder, et al. Heteroduplex mobility assay-guided sequence discovery: Elucidation of the small subunit (18S) rDNA sequences of Pfiesteria piscicida and related dinoflagellates from complex algal culture and environmental sample DNA pools PNAS, April 11, 2000; 97(8): 4303 - 4308. [Abstract] [Full Text] [PDF]
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J. A. Klappenbach, J. M. Dunbar, and T. M. Schmidt rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria Appl. Envir. Microbiol., April 1, 2000; 66(4): 1328 - 1333. [Abstract] [Full Text]
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C. Picard, F. Di Cello, M. Ventura, R. Fani, and A. Guckert Frequency and Biodiversity of 2,4-Diacetylphloroglucinol-Producing Bacteria Isolated from the Maize Rhizosphere at Different Stages of Plant Growth Appl. Envir. Microbiol., March 1, 2000; 66(3): 948 - 955. [Abstract] [Full Text]
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R. J. Davenport, T. P. Curtis, M. Goodfellow, F. M. Stainsby, and M. Bingley Quantitative Use of Fluorescent In Situ Hybridization To Examine Relationships between Mycolic Acid-Containing Actinomycetes and Foaming in Activated Sludge Plants Appl. Envir. Microbiol., March 1, 2000; 66(3): 1158 - 1166. [Abstract] [Full Text]
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A. C. Layton, P. N. Karanth, C. A. Lajoie, A. J. Meyers, I. R. Gregory, R. D. Stapleton, D. E. Taylor, and G. S. Sayler Quantification of Hyphomicrobium Populations in Activated Sludge from an Industrial Wastewater Treatment System as Determined by 16S rRNA Analysis Appl. Envir. Microbiol., March 1, 2000; 66(3): 1167 - 1174. [Abstract] [Full Text]
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E. O. Casamayor, H. Schäfer, L. Bañeras, C. Pedrós-Alió, and G. Muyzer Identification of and Spatio-Temporal Differences between Microbial Assemblages from Two Neighboring Sulfurous Lakes: Comparison by Microscopy and Denaturing Gradient Gel Electrophoresis Appl. Envir. Microbiol., February 1, 2000; 66(2): 499 - 508. [Abstract] [Full Text]
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M. Tonolla, A. Demarta, S. Peduzzi, D. Hahn, and R. Peduzzi In Situ Analysis of Sulfate-Reducing Bacteria Related to Desulfocapsa thiozymogenes in the Chemocline of Meromictic Lake Cadagno (Switzerland) Appl. Envir. Microbiol., February 1, 2000; 66(2): 820 - 824. [Abstract] [Full Text]
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A. Z. Worden, S. W. Chisholm, and B. J. Binder In Situ Hybridization of Prochlorococcus and Synechococcus (Marine Cyanobacteria) spp. with rRNA-Targeted Peptide Nucleic Acid Probes Appl. Envir. Microbiol., January 1, 2000; 66(1): 284 - 289. [Abstract] [Full Text]
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A. Schwiertz, G. Le Blay, and M. Blaut Quantification of Different Eubacterium spp. in Human Fecal Samples with Species-Specific 16S rRNA-Targeted Oligonucleotide Probes Appl. Envir. Microbiol., January 1, 2000; 66(1): 375 - 382. [Abstract] [Full Text]
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C. Zwieb and T. Samuelsson SRPDB (Signal Recognition Particle Database) Nucleic Acids Res., January 1, 2000; 28(1): 171 - 172. [Abstract] [Full Text] [PDF]
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I. Kroes, P. W. Lepp, and D. A. Relman Bacterial diversity within the human subgingival crevice PNAS, December 7, 1999; 96(25): 14547 - 14552. [Abstract] [Full Text] [PDF]
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J. D. Coates, U. Michaelidou, R. A. Bruce, S. M. O'Connor, J. N. Crespi, and L. A. Achenbach Ubiquity and Diversity of Dissimilatory (Per)chlorate-Reducing Bacteria Appl. Envir. Microbiol., December 1, 1999; 65(12): 5234 - 5241. [Abstract] [Full Text]
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J. R. Hanson, J. L. Macalady, D. Harris, and K. M. Scow Linking Toluene Degradation with Specific Microbial Populations in Soil Appl. Envir. Microbiol., December 1, 1999; 65(12): 5403 - 5408. [Abstract] [Full Text]
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M. Ficker, K. Krastel, S. Orlicky, and E. Edwards Molecular Characterization of a Toluene-Degrading Methanogenic Consortium Appl. Envir. Microbiol., December 1, 1999; 65(12): 5576 - 5585. [Abstract] [Full Text]
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K. H. Hansen, B. K. Ahring, and L. Raskin Quantification of Syntrophic Fatty Acid-beta -Oxidizing Bacteria in a Mesophilic Biogas Reactor by Oligonucleotide Probe Hybridization Appl. Envir. Microbiol., November 1, 1999; 65(11): 4767 - 4774. [Abstract] [Full Text]
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A. M. Costello and M. E. Lidstrom Molecular Characterization of Functional and Phylogenetic Genes from Natural Populations of Methanotrophs in Lake Sediments Appl. Envir. Microbiol., November 1, 1999; 65(11): 5066 - 5074. [Abstract] [Full Text]
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H. Urakawa, K. Kita-Tsukamoto, and K. Ohwada Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis Microbiology, November 1, 1999; 145(11): 3305 - 3315. [Abstract] [Full Text] [PDF]
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 T. Allen, P. Shen, L. Samsel, R. Liu, L. Lindahl, and J. M. Zengel Phylogenetic Analysis of L4-Mediated Autogenous Control of the S10 Ribosomal Protein Operon J. Bacteriol., October 1, 1999; 181(19): 6124 - 6132. [Abstract] [Full Text]
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F. Bartels, S. Backhaus, E. R. B. Moore, K. N. Timmis, and B. Hofer Occurrence and expression of glutathione-S-transferase-encoding bphK genes in Burkholderia sp. strain LB400 and other biphenyl-utilizing bacteria Microbiology, October 1, 1999; 145(10): 2821 - 2834. [Abstract] [Full Text] [PDF]
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T. Brinkhoff, S. M. Sievert, J. Kuever, and G. Muyzer Distribution and Diversity of Sulfur-Oxidizing Thiomicrospira spp. at a Shallow-Water Hydrothermal Vent in the Aegean Sea (Milos, Greece) Appl. Envir. Microbiol., September 1, 1999; 65(9): 3843 - 3849. [Abstract] [Full Text]
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A. Galkin, L. Kulakova, H. Ashida, Y. Sawa, and N. Esaki Cold-Adapted Alanine Dehydrogenases from Two Antarctic Bacterial Strains: Gene Cloning, Protein Characterization, and Comparison with Mesophilic and Thermophilic Counterparts Appl. Envir. Microbiol., September 1, 1999; 65(9): 4014 - 4020. [Abstract] [Full Text]
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M. F. Polz, C. Harbison, and C. M. Cavanaugh Diversity and Heterogeneity of Epibiotic Bacterial Communities on the Marine Nematode Eubostrichus dianae Appl. Envir. Microbiol., September 1, 1999; 65(9): 4271 - 4275. [Abstract] [Full Text]
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R.-A. Sandaa, O. Enger, and V. Torsvik Abundance and Diversity of Archaea in Heavy-Metal-Contaminated Soils Appl. Envir. Microbiol., August 1, 1999; 65(8): 3293 - 3297. [Abstract] [Full Text]
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O. Kniemeyer, C. Probian, R. Rosselló-Mora, and J. Harder Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Dimethylmalonate Appl. Envir. Microbiol., August 1, 1999; 65(8): 3319 - 3324. [Abstract] [Full Text]
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A. Fernández, S. Huang, S. Seston, J. Xing, R. Hickey, C. Criddle, and J. Tiedje How Stable Is Stable? Function versus Community Composition Appl. Envir. Microbiol., August 1, 1999; 65(8): 3697 - 3704. [Abstract] [Full Text]
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R. Simmering, B. Kleessen, and M. Blaut Quantification of the Flavonoid-Degrading Bacterium Eubacterium ramulus in Human Fecal Samples with a Species-Specific Oligonucleotide Hybridization Probe Appl. Envir. Microbiol., August 1, 1999; 65(8): 3705 - 3709. [Abstract] [Full Text]
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V. Julliand, A. de Vaux, L. Millet, and G. Fonty Identification of Ruminococcus flavefaciens as the Predominant Cellulolytic Bacterial Species of the Equine Cecum Appl. Envir. Microbiol., August 1, 1999; 65(8): 3738 - 3741. [Abstract] [Full Text]
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