메뉴 건너뛰기




Volumn 39, Issue 14, 2011, Pages

Taxonomic classification of metagenomic shotgun sequences with CARMA3

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CARMA3 METHOD; GENE MUTATION; GENE SEQUENCE; GENETIC DATABASE; GENETIC VARIABILITY; INTERMETHOD COMPARISON; METAGENOME; METAGENOMICS; MULTIGENE FAMILY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; SEQUENCE HOMOLOGY; TAXONOMY;

EID: 80051735813     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr225     Document Type: Article
Times cited : (92)

References (29)
  • 1
    • 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. and Ikemura, T. (2005) Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res., 12, 281-290.
    • (2005) DNA Res. , vol.12 , pp. 281-290
    • Abe, T.1    Sugawara, H.2    Kinouchi, M.3    Kanaya, S.4    Ikemura, T.5
  • 2
    • 62549109116 scopus 로고    scopus 로고
    • TACOA: Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    • Diaz, N.N., Krause, L., Goesmann, A., Niehaus, K. and Nattkemper, T.W. (2009) TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, 10, 56.
    • (2009) BMC Bioinformatics , vol.10 , pp. 56
    • Diaz, N.N.1    Krause, L.2    Goesmann, A.3    Niehaus, K.4    Nattkemper, T.W.5
  • 3
    • 1842332701 scopus 로고    scopus 로고
    • Compositional biases of bacterial genomes and evolutionary implications
    • Karlin, S., Mrazek, J. and Campbell, A.M. (1997) Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol., 179, 3899-3913. (Pubitemid 27259908)
    • (1997) Journal of Bacteriology , vol.179 , Issue.12 , pp. 3899-3913
    • Karlin, S.1    Mrazek, J.2    Campbell, A.M.3
  • 4
    • 33845957530 scopus 로고    scopus 로고
    • Accurate phylogenetic classification of variable-length DNA fragments
    • DOI 10.1038/nmeth976, PII NMETH976
    • McHardy, A.C., Martin, H.G., Tsirigos, A., Hugenholtz, P. and Rigoutsos, I. (2007) Accurate phylogenetic classification of variable-length dna fragments. Nat. Methods, 4, 63-72. (Pubitemid 46029478)
    • (2007) Nature Methods , vol.4 , Issue.1 , pp. 63-72
    • McHardy, A.C.1    Martin, H.G.2    Tsirigos, A.3    Hugenholtz, P.4    Rigoutsos, I.5
  • 5
    • 13244253777 scopus 로고    scopus 로고
    • TETRA: A web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in dna sequences
    • Teeling, H., Waldmann, J., Lombardot, T., Bauer, M. and Glockner, F.O. (2004) TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in dna sequences. BMC Bioinformatics, 5, 163.
    • (2004) BMC Bioinformatics , vol.5 , pp. 163
    • Teeling, H.1    Waldmann, J.2    Lombardot, T.3    Bauer, M.4    Glockner, F.O.5
  • 6
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S.R. (1998) Profile hidden markov models (review). Bioinformatics, 14, 755-763. (Pubitemid 28552108)
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 755-763
    • Eddy, S.R.1
  • 8
    • 0027399530 scopus 로고
    • Identification of protein coding regions by database similarity search
    • DOI 10.1038/ng0393-266
    • Gish, W. and States, D.J. (1993) Identification of protein coding regions by database similarity search. Nat. Genet., 3, 266-272. (Pubitemid 23096565)
    • (1993) Nature Genetics , vol.3 , Issue.3 , pp. 266-272
    • Gish, W.1    States, D.J.2
  • 10
    • 74049132798 scopus 로고    scopus 로고
    • WebCARMA: A web application for the functional and taxonomic classification of unassembled metagenomic reads
    • Gerlach, W., Junemann, S., Tille, F., Goesmann, A. and Stoye, J. (2009) WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics, 10, 430.
    • (2009) BMC Bioinformatics , vol.10 , pp. 430
    • Gerlach, W.1    Junemann, S.2    Tille, F.3    Goesmann, A.4    Stoye, J.5
  • 12
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • DOI 10.1101/gr.5969107
    • Huson, D.H., Auch, A.F., Qi, J. and Schuster, S.C. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386. (Pubitemid 46376747)
    • (2007) Genome Research , vol.17 , Issue.3 , pp. 377-386
    • Huson, D.H.1    Auch, A.F.2    Qi, J.3    Schuster, S.C.4
  • 13
    • 67649887316 scopus 로고    scopus 로고
    • SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
    • Haque, M.M., Ghosh, T.S., Komanduri, D. and Mande, S.S. (2009) SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences. Bioinformatics, 25, 1722-1730.
    • (2009) Bioinformatics , vol.25 , pp. 1722-1730
    • Haque, M.M.1    Ghosh, T.S.2    Komanduri, D.3    Mande, S.S.4
  • 15
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 17
    • 54949137701 scopus 로고    scopus 로고
    • Metasim: A sequencing simulator for genomics and metagenomics
    • Richter, D.C., Ott, F., Auch, A.F., Schmid, R. and Huson, D.H. (2008) Metasim: a sequencing simulator for genomics and metagenomics. PLoS ONE, 3, e3373.
    • (2008) PLoS ONE , vol.3
    • Richter, D.C.1    Ott, F.2    Auch, A.F.3    Schmid, R.4    Huson, D.H.5
  • 18
    • 49949108153 scopus 로고    scopus 로고
    • The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology
    • Schluter, A., Bekel, T., Diaz, N.N., Dondrup, M., Eichenlaub, R., Gartemann, K.-H., Krahn, I., Krause, L., Kromeke, H., Kruse, O. et al. (2008) The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J. Biotechnol., 136, 77-90.
    • (2008) J. Biotechnol. , vol.136 , pp. 77-90
    • Schluter, A.1    Bekel, T.2    Diaz, N.N.3    Dondrup, M.4    Eichenlaub, R.5    Gartemann, K.-H.6    Krahn, I.7    Krause, L.8    Kromeke, H.9    Kruse, O.10
  • 21
    • 67349232764 scopus 로고    scopus 로고
    • Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing
    • Krober, M., Bekel, T., Diaz, N.N., Goesmann, A., Jaenicke, S., Krause, L., Miller, D., Runte, K.J., Viehover, P., Puhler, A. et al. (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J. Biotechnol., 142, 38-49.
    • (2009) J. Biotechnol. , vol.142 , pp. 38-49
    • Krober, M.1    Bekel, T.2    Diaz, N.N.3    Goesmann, A.4    Jaenicke, S.5    Krause, L.6    Miller, D.7    Runte, K.J.8    Viehover, P.9    Puhler, A.10
  • 22
    • 0036181778 scopus 로고    scopus 로고
    • Exploring prokaryotic diversity in the genomic era
    • Hugenholtz, P. (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol., 3.
    • (2002) Genome Biol. , vol.3
    • Hugenholtz, P.1
  • 23
    • 2342586717 scopus 로고    scopus 로고
    • 16 S rDNA primers and the unbiased assessment of thermophile diversity
    • DOI 10.1042/BST0320218
    • Baker, G.C. and Cowan, D.A. (2004) 16S rDNA primers and the unbiased assessment of thermophile diversity. Biochem. Soc. Trans., 32(Pt 2), 218-221. (Pubitemid 38582094)
    • (2004) Biochemical Society Transactions , vol.32 , Issue.2 , pp. 218-221
    • Baker, G.C.1    Cowan, D.A.2
  • 26
    • 2942702110 scopus 로고    scopus 로고
    • Clostridium bartlettii sp. nov., isolated from human faeces
    • DOI 10.1016/j.anaerobe.2004.04.004, PII S1075996404000319
    • Song, Y.L., Liu, C.X., McTeague, M., Summanen, P. and Finegold, S.M. (2004) Clostridium bartlettii sp. nov., isolated from human faeces. Anaerobe, 10, 179-184. (Pubitemid 38789119)
    • (2004) Anaerobe , vol.10 , Issue.3 , pp. 179-184
    • Song, Y.L.1    Liu, C.X.2    McTeague, M.3    Summanen, P.4    Finegold, S.M.5
  • 27
    • 0036739483 scopus 로고    scopus 로고
    • Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces
    • Duncan, S.H., Hold, G.L., Barcenilla, A., Stewart, C.S. and Flint, H.J. (2002) Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. Int. J. Syst. Evol. Microbiol., 52(Pt 5), 1615-1620.
    • (2002) Int. J. Syst. Evol. Microbiol. , vol.52 , Issue.PART 5 , pp. 1615-1620
    • Duncan, S.H.1    Hold, G.L.2    Barcenilla, A.3    Stewart, C.S.4    Flint, H.J.5
  • 28
    • 79952765513 scopus 로고    scopus 로고
    • Microbes and health sackler colloquium: Substrate-driven gene expression in roseburia inulinivorans: Importance of inducible enzymes in the utilization of inulin and starch
    • Scott, K.P., Martin, J.C., Chassard, C., Clerget, M., Potrykus, J., Campbell, G., Mayer, C.-D., Young, P., Rucklidge, G., Ramsay, A.G. et al. (2010) Microbes and health sackler colloquium: substrate-driven gene expression in roseburia inulinivorans: Importance of inducible enzymes in the utilization of inulin and starch. Proc. Natl Acad. Sci. USA, 108, 4672-4679.
    • (2010) Proc. Natl Acad. Sci. USA , vol.108 , pp. 4672-4679
    • Scott, K.P.1    Martin, J.C.2    Chassard, C.3    Clerget, M.4    Potrykus, J.5    Campbell, G.6    Mayer, C.-D.7    Young, P.8    Rucklidge, G.9    Ramsay, A.G.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.