Bioinformatics Advance Access published online on April 8, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth226
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 ComBinE group, Advanced Computational Modelling Centre, The University of Queensland, Brisbane 4072, Australia
* To whom correspondence should be addressed. E-mail: huber{at}maths.uq.edu.au.
Summary: Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Availability: Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl.
Revised January 28, 2004
Accepted January 28, 2004
Applications note
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
2 Department of Environmental Science, Policy and Management, 151 Hilgard Hall, University of California Berkeley, Berkeley, CA 94720-3110, USA
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G. W. Weidler, M. Dornmayr-Pfaffenhuemer, F. W. Gerbl, W. Heinen, and H. Stan-Lotter Communities of Archaea and Bacteria in a Subsurface Radioactive Thermal Spring in the Austrian Central Alps, and Evidence of Ammonia-Oxidizing Crenarchaeota Appl. Envir. Microbiol., January 1, 2007; 73(1): 259 - 270. [Abstract] [Full Text] [PDF]
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S. Nakagawa, F. Inagaki, Y. Suzuki, B. O. Steinsbu, M. A. Lever, K. Takai, B. Engelen, Y. Sako, C. G. Wheat, K. Horikoshi, et al. Microbial Community in Black Rust Exposed to Hot Ridge Flank Crustal Fluids Appl. Envir. Microbiol., October 1, 2006; 72(10): 6789 - 6799. [Abstract] [Full Text] [PDF]
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Y. Hongoh, P. Deevong, S. Hattori, T. Inoue, S. Noda, N. Noparatnaraporn, T. Kudo, and M. Ohkuma Phylogenetic Diversity, Localization, and Cell Morphologies of Members of the Candidate Phylum TG3 and a Subphylum in the Phylum Fibrobacteres, Recently Discovered Bacterial Groups Dominant in Termite Guts Appl. Envir. Microbiol., October 1, 2006; 72(10): 6780 - 6788. [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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W. J. Brazelton, M. O. Schrenk, D. S. Kelley, and J. A. Baross Methane- and Sulfur-Metabolizing Microbial Communities Dominate the Lost City Hydrothermal Field Ecosystem Appl. Envir. Microbiol., September 1, 2006; 72(9): 6257 - 6270. [Abstract] [Full Text] [PDF]
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E. L. Brodie, T. Z. DeSantis, D. C. Joyner, S. M. Baek, J. T. Larsen, G. L. Andersen, T. C. Hazen, P. M. Richardson, D. J. Herman, T. K. Tokunaga, et al. Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation Appl. Envir. Microbiol., September 1, 2006; 72(9): 6288 - 6298. [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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S. Lin, H. Zhang, Y. Hou, L. Miranda, and D. Bhattacharya Development of a Dinoflagellate-Oriented PCR Primer Set Leads to Detection of Picoplanktonic Dinoflagellates from Long Island Sound Appl. Envir. Microbiol., August 1, 2006; 72(8): 5626 - 5630. [Abstract] [Full Text] [PDF]
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T. Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl. Envir. Microbiol., July 1, 2006; 72(7): 5069 - 5072. [Abstract] [Full Text] [PDF]
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H. Sanguin, B. Remenant, A. Dechesne, J. Thioulouse, T. M. Vogel, X. Nesme, Y. Moenne-Loccoz, and G. L. Grundmann Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities. Appl. Envir. Microbiol., June 1, 2006; 72(6): 4302 - 4312. [Abstract] [Full Text] [PDF]
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R. E. Ley, J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A. Bryant, M. L. Sogin, and N. R. Pace Unexpected diversity and complexity of the guerrero negro hypersaline microbial mat. Appl. Envir. Microbiol., May 1, 2006; 72(5): 3685 - 3695. [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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J. Kirkpatrick, B. Oakley, C. Fuchsman, S. Srinivasan, J. T. Staley, and J. W. Murray Diversity and Distribution of Planctomycetes and Related Bacteria in the Suboxic Zone of the Black Sea Appl. Envir. Microbiol., April 1, 2006; 72(4): 3079 - 3083. [Abstract] [Full Text] [PDF]
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S. N. Dedysh, T. A. Pankratov, S. E. Belova, I. S. Kulichevskaya, and W. Liesack Phylogenetic analysis and in situ identification of bacteria community composition in an acidic sphagnum peat bog. Appl. Envir. Microbiol., March 1, 2006; 72(3): 2110 - 2117. [Abstract] [Full Text] [PDF]
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Y. Taprab, T. Johjima, Y. Maeda, S. Moriya, S. Trakulnaleamsai, N. Noparatnaraporn, M. Ohkuma, and T. Kudo Symbiotic Fungi Produce Laccases Potentially Involved in Phenol Degradation in Fungus Combs of Fungus-Growing Termites in Thailand Appl. Envir. Microbiol., December 1, 2005; 71(12): 7696 - 7704. [Abstract] [Full Text] [PDF]
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K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies Appl. Envir. Microbiol., December 1, 2005; 71(12): 7724 - 7736. [Abstract] [Full Text] [PDF]
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T. E. Freitag, L. Chang, C. D. Clegg, and J. I. Prosser Influence of Inorganic Nitrogen Management Regime on the Diversity of Nitrite-Oxidizing Bacteria in Agricultural Grassland Soils Appl. Envir. Microbiol., December 1, 2005; 71(12): 8323 - 8334. [Abstract] [Full Text] [PDF]
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D. P. Moser, T. M. Gihring, F. J. Brockman, J. K. Fredrickson, D. L. Balkwill, M. E. Dollhopf, B. S. Lollar, L. M. Pratt, E. Boice, G. Southam, et al. Desulfotomaculum and Methanobacterium spp. Dominate a 4- to 5-Kilometer-Deep Fault Appl. Envir. Microbiol., December 1, 2005; 71(12): 8773 - 8783. [Abstract] [Full Text] [PDF]
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A. K. Dunn and E. V. Stabb Culture-Independent Characterization of the Microbiota of the Ant Lion Myrmeleon mobilis (Neuroptera: Myrmeleontidae) Appl. Envir. Microbiol., December 1, 2005; 71(12): 8784 - 8794. [Abstract] [Full Text] [PDF]
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S. von der Heyden and T. Cavalier-Smith Culturing and environmental DNA sequencing uncover hidden kinetoplastid biodiversity and a major marine clade within ancestrally freshwater Neobodo designis Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2605 - 2621. [Abstract] [Full Text] [PDF]
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Y. Hongoh, P. Deevong, T. Inoue, S. Moriya, S. Trakulnaleamsai, M. Ohkuma, C. Vongkaluang, N. Noparatnaraporn, and T. Kudo Intra- and Interspecific Comparisons of Bacterial Diversity and Community Structure Support Coevolution of Gut Microbiota and Termite Host Appl. Envir. Microbiol., November 1, 2005; 71(11): 6590 - 6599. [Abstract] [Full Text] [PDF]
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K. B. Sorensen, D. E. Canfield, A. P. Teske, and A. Oren Community Composition of a Hypersaline Endoevaporitic Microbial Mat Appl. Envir. Microbiol., November 1, 2005; 71(11): 7352 - 7365. [Abstract] [Full Text] [PDF]
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J. Slapeta, D. Moreira, and P. Lopez-Garcia The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes Proc R Soc B, October 7, 2005; 272(1576): 2073 - 2081. [Abstract] [Full Text] [PDF]
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H. M. Simon, C. E. Jahn, L. T. Bergerud, M. K. Sliwinski, P. J. Weimer, D. K. Willis, and R. M. Goodman Cultivation of Mesophilic Soil Crenarchaeotes in Enrichment Cultures from Plant Roots Appl. Envir. Microbiol., August 1, 2005; 71(8): 4751 - 4760. [Abstract] [Full Text] [PDF]
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C. F. V. Hobel, V. T. Marteinsson, G. O. Hreggvidsson, and J. K. Kristjansson Investigation of the Microbial Ecology of Intertidal Hot Springs by Using Diversity Analysis of 16S rRNA and Chitinase Genes Appl. Envir. Microbiol., May 1, 2005; 71(5): 2771 - 2776. [Abstract] [Full Text] [PDF]
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