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Volumn 4, Issue 1, 2007, Pages 63-72

Accurate phylogenetic classification of variable-length DNA fragments

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

EID: 33845957530     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth976     Document Type: Article
Times cited : (394)

References (35)
  • 1
    • 11144354360 scopus 로고    scopus 로고
    • Environmental genome shotgun sequencing of the Sargasso Sea
    • Venter, J.C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004).
    • (2004) Science , vol.304 , pp. 66-74
    • Venter, J.C.1
  • 2
    • 20244376755 scopus 로고    scopus 로고
    • Comparative metagenomics of microbial communities
    • Tringe, S.G. et al. Comparative metagenomics of microbial communities. Science 308, 554-557 (2005).
    • (2005) Science , vol.308 , pp. 554-557
    • Tringe, S.G.1
  • 3
    • 1542377296 scopus 로고    scopus 로고
    • Community structure and metabolism through reconstruction of microbial genomes from the environment
    • Tyson, G.W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43 (2004).
    • (2004) Nature , vol.428 , pp. 37-43
    • Tyson, G.W.1
  • 4
    • 0036181778 scopus 로고    scopus 로고
    • Exploring prokaryotic diversity in the genomic era
    • REVIEWS0003
    • Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol., 3, REVIEWS0003 (2002).
    • (2002) Genome Biol , vol.3
    • Hugenholtz, P.1
  • 5
    • 0001271789 scopus 로고
    • Phylogenetic structure of the prokaryotic domain: The primary kingdoms
    • Woese, C.R. & Fox, G.E. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. USA 74, 5088-5090 (1977).
    • (1977) Proc. Natl. Acad. Sci. USA , vol.74 , pp. 5088-5090
    • Woese, C.R.1    Fox, G.E.2
  • 6
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese, C.R. Bacterial evolution. Microbiol. Rev. 51, 221-271 (1987).
    • (1987) Microbiol. Rev. , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 8
    • 0348044549 scopus 로고    scopus 로고
    • Genome trees constructed using five different approaches suggest new major bacterial clades
    • Wolf, Y.I., Rogozin, I.B., Grishin, N.V., Tatusov, R.L. & Koonin, E.V. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1, 8 (2001).
    • (2001) BMC Evol. Biol. , vol.1 , pp. 8
    • Wolf, Y.I.1    Rogozin, I.B.2    Grishin, N.V.3    Tatusov, R.L.4    Koonin, E.V.5
  • 9
    • 33644700003 scopus 로고    scopus 로고
    • Toward automatic reconstruction of a highly resolved tree of life
    • Ciccarelli, F.D. et al. Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287 (2006).
    • (2006) Science , vol.311 , pp. 1283-1287
    • Ciccarelli, F.D.1
  • 10
    • 13444304367 scopus 로고    scopus 로고
    • The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis
    • Cole, J.R. et al. The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33, D294-D296 (2005).
    • (2005) Nucleic Acids Res , vol.33
    • Cole, J.R.1
  • 11
    • 33749858537 scopus 로고    scopus 로고
    • Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
    • Garcìa Martin, H. et al. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 24, 1263-1269 (2006).
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1263-1269
    • Garcìa Martin, H.1
  • 12
    • 4344670204 scopus 로고    scopus 로고
    • Application of tetranucleotide frequencies for the assignment of genomic fragments
    • Teeling, H., Meyerdierks, A., Bauer, M., Amann, R. & Glockner, F.D. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ. Microbiol. 6, 938-947 (2004).
    • (2004) Environ. Microbiol. , vol.6 , pp. 938-947
    • Teeling, H.1    Meyerdierks, A.2    Bauer, M.3    Amann, R.4    Glockner, F.D.5
  • 13
    • 23944525404 scopus 로고    scopus 로고
    • Computational improvements reveal great bacterial diversity and high metal toxicity in soil
    • Gans, J., Wolinsky, M. & Dunbar, J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387-1390 (2005).
    • (2005) Science , vol.309 , pp. 1387-1390
    • Gans, J.1    Wolinsky, M.2    Dunbar, J.3
  • 14
    • 0029060923 scopus 로고
    • Dinucleotide relative abundance extremes: A genomic signature
    • Karlin, S. & Burge, C. Dinucleotide relative abundance extremes: A genomic signature. Trends Genet. 11, 283-290 (1995).
    • (1995) Trends Genet , vol.11 , pp. 283-290
    • Karlin, S.1    Burge, C.2
  • 15
    • 0030923586 scopus 로고    scopus 로고
    • Compositional differences within and between eukaryotic genomes
    • Karlin, S. & Mrazek, J. Compositional differences within and between eukaryotic genomes. Proc. Natl. Acad. Sci. USA 94, 10227-10232 (1997).
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 10227-10232
    • Karlin, S.1    Mrazek, J.2
  • 16
    • 0032823783 scopus 로고    scopus 로고
    • Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences
    • Deschavanne, P.J., Giron, A., Vilain, J., Fagot, G. & Fertil, B. Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences. Mol. Biol. Evol. 16, 1391-1399 (1999).
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1391-1399
    • Deschavanne, P.J.1    Giron, A.2    Vilain, J.3    Fagot, G.4    Fertil, B.5
  • 17
    • 0032582395 scopus 로고    scopus 로고
    • Genes from nine genomes are separated into their organisms in the dinucleotide composition space
    • Nakashima, H., Ota, M., Nishikawa, K. & Ooi, T. Genes from nine genomes are separated into their organisms in the dinucleotide composition space. DNA Res. 5, 251-259 (1998).
    • (1998) DNA Res , vol.5 , pp. 251-259
    • Nakashima, H.1    Ota, M.2    Nishikawa, K.3    Ooi, T.4
  • 18
    • 0034887748 scopus 로고    scopus 로고
    • Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier
    • Sandberg, R. et al. Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res. 11, 1404-1409 (2001).
    • (2001) Genome Res , vol.11 , pp. 1404-1409
    • Sandberg, R.1
  • 19
    • 0642374412 scopus 로고    scopus 로고
    • A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: Self-organizing map of oligonucleotide frequency
    • Abe, T. et al. A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: Self-organizing map of oligonucleotide frequency. Genome Inform. Ser. Workshop Genome Inform. 13, 12-20 (2002).
    • (2002) Genome Inform. Ser. Workshop Genome Inform , vol.13 , pp. 12-20
    • Abe, T.1
  • 20
    • 0037315735 scopus 로고    scopus 로고
    • Evolutionary implications of microbial genome tetranucleotide frequency biases
    • Pride, D.T., Meinersmann, R.J., Wassenaar, T.M. & Blaser, M.J. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 13, 145-158 (2003).
    • (2003) Genome Res , vol.13 , pp. 145-158
    • Pride, D.T.1    Meinersmann, R.J.2    Wassenaar, T.M.3    Blaser, M.J.4
  • 21
    • 28844458060 scopus 로고    scopus 로고
    • Exploration of phylogenetic data using a global sequence analysis method
    • Chapus, C. et al. Exploration of phylogenetic data using a global sequence analysis method. BMC Evol. Biol. 5, 63 (2005).
    • (2005) BMC Evol. Biol. , vol.5 , pp. 63
    • Chapus, C.1
  • 22
    • 33646569088 scopus 로고    scopus 로고
    • Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples
    • Abe, T., Sugawara, H., Kinouchi, M., Kanaya, S. & Ikemura, T. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res. 12, 281-290 (2005).
    • (2005) DNA Res , vol.12 , pp. 281-290
    • Abe, T.1    Sugawara, H.2    Kinouchi, M.3    Kanaya, S.4    Ikemura, T.5
  • 23
    • 33745595097 scopus 로고    scopus 로고
    • Using pyrosequencing to shed light on deep mine microbial ecology
    • Edwards, R.A. et al. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7, 57 (2006).
    • (2006) BMC Genomics , vol.7 , pp. 57
    • Edwards, R.A.1
  • 24
  • 25
    • 0036796799 scopus 로고    scopus 로고
    • Synonymous codon usage is subject to selection in thermophilic bacteria
    • Lynn, D.J., Singer, G.A. & Hickey, D.A. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30, 4272-4277 (2002).
    • (2002) Nucleic Acids Res , vol.30 , pp. 4272-4277
    • Lynn, D.J.1    Singer, G.A.2    Hickey, D.A.3
  • 26
    • 34248374277 scopus 로고    scopus 로고
    • A putative RNA-interference-based immune system in prokaryotes: Computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
    • Makarova, K.S., Grishin, N.V., Shabalina, S.A., Wolf, Y.I. & Koonin, E.V. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct 1, 7 (2006).
    • (2006) Biol Direct , vol.1 , pp. 7
    • Makarova, K.S.1    Grishin, N.V.2    Shabalina, S.A.3    Wolf, Y.I.4    Koonin, E.V.5
  • 27
    • 19144362371 scopus 로고    scopus 로고
    • Microbial community genomics in the ocean
    • DeLong, E.F. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3, 459-469 (2005).
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 459-469
    • DeLong, E.F.1
  • 28
    • 33745127708 scopus 로고    scopus 로고
    • Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations
    • Kalyuzhnaya, M.G. et al. Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations. Appl. Environ. Microbiol. 72, 4293-4301 (2006).
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 4293-4301
    • Kalyuzhnaya, M.G.1
  • 29
    • 33745085561 scopus 로고    scopus 로고
    • Sequencing genomes from single cells by polymerase cloning
    • Zhang, K. et al. Sequencing genomes from single cells by polymerase cloning. Nat. Biotechnol. 24, 680-686 (2006).
    • (2006) Nat. Biotechnol. , vol.24 , pp. 680-686
    • Zhang, K.1
  • 30
    • 0033529862 scopus 로고    scopus 로고
    • Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA
    • Campbell, A., Mrazek, J. & Karlin, S. Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc. Natl. Acad. Sci. USA 96, 9184-9189 (1999).
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9184-9189
    • Campbell, A.1    Mrazek, J.2    Karlin, S.3
  • 32
    • 0033609333 scopus 로고    scopus 로고
    • Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
    • Nelson, K.E. et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329 (1999).
    • (1999) Nature , vol.399 , pp. 323-329
    • Nelson, K.E.1
  • 33
    • 13944251386 scopus 로고    scopus 로고
    • A new computational method for the detection of horizontal gene transfer events
    • Tsirigos, A. & Rigoutsos, I. A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res. 33, 922-933 (2005).
    • (2005) Nucleic Acids Res , vol.33 , pp. 922-933
    • Tsirigos, A.1    Rigoutsos, I.2
  • 34
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek, R. et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691-5702 (2005).
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1
  • 35
    • 0035162272 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Wheeler, D.L. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 29, 11-16 (2001).
    • (2001) Nucleic Acids Res , vol.29 , pp. 11-16
    • Wheeler, D.L.1


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