메뉴 건너뛰기




Volumn 31, Issue 6, 2015, Pages 817-824

Taxator-tk: Precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 84925243945     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu745     Document Type: Article
Times cited : (109)

References (37)
  • 1
    • 84879678051 scopus 로고    scopus 로고
    • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    • Albertsen, M. et al. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol., 31, 533-538.
    • (2013) Nat. Biotechnol. , vol.31 , pp. 533-538
    • Albertsen, M.1
  • 2
    • 84908597294 scopus 로고    scopus 로고
    • Binning metagenomic contigs by coverage and composition
    • Alneberg, J. et al. (2014) Binning metagenomic contigs by coverage and composition. Nat. Methods, 11, 1144-1146.
    • (2014) Nat. Methods , vol.11 , pp. 1144-1146
    • Alneberg, J.1
  • 3
    • 84861180216 scopus 로고    scopus 로고
    • Joint analysis of multiple metagenomic samples
    • Baran, Y. and Halperin, E. (2012) Joint analysis of multiple metagenomic samples. PLoS Comput. Biol., 8, e1002373.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002373
    • Baran, Y.1    Halperin, E.2
  • 4
    • 79955456912 scopus 로고    scopus 로고
    • Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood
    • Berger, S.A. et al. (2011) Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol., 60, 291-302.
    • (2011) Syst. Biol. , vol.60 , pp. 291-302
    • Berger, S.A.1
  • 5
    • 79955611184 scopus 로고    scopus 로고
    • PhymmBL expanded: Confidence scores, custom databases, parallelization and more
    • Brady, A. and Salzberg, S. (2011) PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat. Methods, 8, 367.
    • (2011) Nat. Methods , vol.8 , pp. 367
    • Brady, A.1    Salzberg, S.2
  • 6
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+: Architecture and applications
    • Camacho, C. et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 7
    • 84887265124 scopus 로고    scopus 로고
    • Reconstructing the genomic content of microbiome taxa through shotgunmetagenomic deconvolution
    • Carr, R. et al. (2013) Reconstructing the genomic content of microbiome taxa through shotgunmetagenomic deconvolution. PLoS Comput. Biol., 9, e1003292.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003292
    • Carr, R.1
  • 8
    • 84895751645 scopus 로고    scopus 로고
    • PhyloSift: Phylogenetic analysis of genomes and metagenomes
    • Darling, A.E. et al. (2014) PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ, 2, e243.
    • (2014) PeerJ , vol.2 , pp. e243
    • Darling, A.E.1
  • 9
    • 84870035320 scopus 로고    scopus 로고
    • Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
    • Dröge, J. and McHardy, A.C. (2012) Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief. Bioinform., 13, 646-655.
    • (2012) Brief. Bioinform. , vol.13 , pp. 646-655
    • Dröge, J.1    McHardy, A.C.2
  • 10
    • 77649140807 scopus 로고    scopus 로고
    • Parameters for accurate genome alignment
    • Frith, M.C. et al. (2010) Parameters for accurate genome alignment. BMC Bioinformatics, 11, 80.
    • (2010) BMC Bioinformatics , vol.11 , pp. 80
    • Frith, M.C.1
  • 11
    • 80051735813 scopus 로고    scopus 로고
    • Taxonomic classification of metagenomic shotgun sequences with CARMA3
    • Gerlach, W. and Stoye, J. (2011) Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic Acids Res., 39, e91.
    • (2011) Nucleic Acids Res. , vol.39 , pp. e91
    • Gerlach, W.1    Stoye, J.2
  • 13
    • 79251587455 scopus 로고    scopus 로고
    • Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
    • Hess, M. et al. (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science, 331, 463-467.
    • (2011) Science , vol.331 , pp. 463-467
    • Hess, M.1
  • 14
    • 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, 1-8.
    • (2002) Genome Biol. , vol.3 , pp. 1-8
    • Hugenholtz, P.1
  • 15
    • 80052549504 scopus 로고    scopus 로고
    • Integrative analysis of environmental sequences using MEGAN4
    • Huson, D.H. et al. (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res., 21, 1552-1560.
    • (2011) Genome Res. , vol.21 , pp. 1552-1560
    • Huson, D.H.1
  • 16
    • 84861729132 scopus 로고    scopus 로고
    • PIRS: Profile-based Illumina pair-end reads simulator
    • Hu, X. et al. (2012) pIRS: profile-based Illumina pair-end reads simulator. Bioinformatics, 28, 1533-1535.
    • (2012) Bioinformatics , vol.28 , pp. 1533-1535
    • Hu, X.1
  • 17
    • 84856659328 scopus 로고    scopus 로고
    • Untangling genomes from metagenomes: Revealing an uncultured class of marine Euryarchaeota
    • Iverson, V. et al. (2012) Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science, 335, 587-590.
    • (2012) Science , vol.335 , pp. 587-590
    • Iverson, V.1
  • 18
    • 84878581087 scopus 로고    scopus 로고
    • Next generation sequencing technologies and the changing landscape of phage genomics
    • Klumpp, J. et al. (2012) Next generation sequencing technologies and the changing landscape of phage genomics. Bacteriophage, 2, 190-199.
    • (2012) Bacteriophage , vol.2 , pp. 190-199
    • Klumpp, J.1
  • 19
    • 84882651790 scopus 로고    scopus 로고
    • Quikr: A method for rapid reconstruction of bacterial communities via compressive sensing
    • Koslicki, D. et al. (2013) Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. Bioinformatics, 29, 2096-2102.
    • (2013) Bioinformatics , vol.29 , pp. 2096-2102
    • Koslicki, D.1
  • 20
    • 57349141505 scopus 로고    scopus 로고
    • A bioinformatician's guide to metagenomics
    • Kunin, V. et al. (2008) A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev., 72, 557-578.
    • (2008) Microbiol. Mol. Biol. Rev. , vol.72 , pp. 557-578
    • Kunin, V.1
  • 21
    • 84871725334 scopus 로고    scopus 로고
    • Metagenomic abundance estimation and diagnostic testing on species level
    • Lindner, M.S. and Renard, B.Y. (2013) Metagenomic abundance estimation and diagnostic testing on species level. Nucleic Acids Res., 41, e10.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e10
    • Lindner, M.S.1    Renard, B.Y.2
  • 22
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Luo, R. et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 18.
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1
  • 23
    • 77958610660 scopus 로고    scopus 로고
    • Pplacer: Linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen, F.A. et al. (2010) pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11, 538.
    • (2010) BMC Bioinformatics , vol.11 , pp. 538
    • Matsen, F.A.1
  • 24
    • 84860334363 scopus 로고    scopus 로고
    • Reconciling taxonomy and phylogenetic inference: Formalism and algorithms for describing discord and inferring taxonomic roots
    • Matsen, F.A. and Gallagher, A. (2012) Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. Algorithms Mol. Biol., 7, 8.
    • (2012) Algorithms Mol. Biol. , vol.7 , pp. 8
    • Matsen, F.A.1    Gallagher, A.2
  • 25
    • 34249794257 scopus 로고    scopus 로고
    • Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
    • Mavromatis, K. et al. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Methods, 4, 495-500.
    • (2007) Nat. Methods , vol.4 , pp. 495-500
    • Mavromatis, K.1
  • 26
    • 33845957530 scopus 로고    scopus 로고
    • Accurate phylogenetic classification of variablelength DNA fragments
    • McHardy, A.C. et al. (2007) Accurate phylogenetic classification of variablelength DNA fragments. Nat. Methods, 4, 63-72.
    • (2007) Nat. Methods , vol.4 , pp. 63-72
    • McHardy, A.C.1
  • 27
    • 67649887316 scopus 로고    scopus 로고
    • SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
    • Monzoorul Haque, M. et al. (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
    • Monzoorul Haque, M.1
  • 28
    • 79952124952 scopus 로고    scopus 로고
    • Taxonomic metagenome sequence assignment with structured output models
    • Patil, K.R. et al. (2011) Taxonomic metagenome sequence assignment with structured output models. Nat. Methods, 8, 191-192.
    • (2011) Nat. Methods , vol.8 , pp. 191-192
    • Patil, K.R.1
  • 29
    • 79960931485 scopus 로고    scopus 로고
    • Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies
    • Pope, P.B. et al. (2011) Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science, 333, 646-648.
    • (2011) Science , vol.333 , pp. 646-648
    • Pope, P.B.1
  • 30
    • 10944226351 scopus 로고    scopus 로고
    • Metagenomics: Genomic analysis of microbial communities
    • Riesenfeld, C.S. et al. (2004) Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet., 38, 525-552.
    • (2004) Annu. Rev. Genet. , vol.38 , pp. 525-552
    • Riesenfeld, C.S.1
  • 31
    • 58149200954 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Sayers, E.W. et al. (2009) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 37, D5-D15.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D5-D15
    • Sayers, E.W.1
  • 32
    • 84871732071 scopus 로고    scopus 로고
    • Genomic variation landscape of the human gut microbiome
    • Schloissnig, S. et al. (2013) Genomic variation landscape of the human gut microbiome. Nature, 493, 45-50.
    • (2013) Nature , vol.493 , pp. 45-50
    • Schloissnig, S.1
  • 33
    • 84864440400 scopus 로고    scopus 로고
    • Metagenomic microbial community profiling using unique clade-specific marker genes
    • Segata, N. et al. (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods, 9, 811-814.
    • (2012) Nat. Methods , vol.9 , pp. 811-814
    • Segata, N.1
  • 34
    • 84903837939 scopus 로고    scopus 로고
    • FOCUS: An alignment-free model to identify organisms in metagenomes using non-negative least squares
    • Silva, G.G.Z. et al. (2014) FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. PeerJ, 2, e425.
    • (2014) PeerJ , vol.2 , pp. e425
    • Silva, G.G.Z.1
  • 35
    • 77955179934 scopus 로고    scopus 로고
    • MLTreeMap-accurate maximum likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
    • Stark, M. et al. (2010) MLTreeMap-accurate maximum likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics, 11, 461.
    • (2010) BMC Genomics , vol.11 , pp. 461
    • Stark, M.1
  • 36
    • 84888884475 scopus 로고    scopus 로고
    • Metagenomic species profiling using universal phylogenetic marker genes
    • Sunagawa, S. et al. (2013) Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods, 10, 1196-1199.
    • (2013) Nat. Methods , vol.10 , pp. 1196-1199
    • Sunagawa, S.1
  • 37
    • 84899090573 scopus 로고    scopus 로고
    • Kraken: Ultrafast metagenomic sequence classification using exact alignments
    • Wood, D.E. and Salzberg, S.L. (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol., 15, R46.
    • (2014) Genome Biol. , vol.15 , pp. R46
    • Wood, D.E.1    Salzberg, S.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.