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Volumn 13, Issue 1, 2015, Pages

MetAnnotate: Function-specific taxonomic profiling and comparison of metagenomes

Author keywords

Metagenomics; Microbiome; Next generation sequencing; Taxonomic profiling

Indexed keywords

CYANOCOBALAMIN;

EID: 84946406423     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/s12915-015-0195-4     Document Type: Article
Times cited : (28)

References (36)
  • 1
    • 10344227692 scopus 로고    scopus 로고
    • Metagenomics: application of genomics to uncultured microorganisms
    • Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669-85.
    • (2004) Microbiol Mol Biol Rev , vol.68 , pp. 669-685
    • Handelsman, J.1
  • 2
    • 35748959318 scopus 로고    scopus 로고
    • What's in the mix: phylogenetic classification of metagenome sequence samples
    • McHardy AC, Rigoutsos I. What's in the mix: phylogenetic classification of metagenome sequence samples. Curr Opin Microbiol. 2007;10:499-503.
    • (2007) Curr Opin Microbiol , vol.10 , pp. 499-503
    • McHardy, A.C.1    Rigoutsos, I.2
  • 3
    • 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, Glöckner FO. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics. 2004;5:163.
    • (2004) BMC Bioinformatics , vol.5 , pp. 163
    • Teeling, H.1    Waldmann, J.2    Lombardot, T.3    Bauer, M.4    Glöckner, F.O.5
  • 5
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods. 2009;6:673-6.
    • (2009) Nat Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 9
    • 0034992826 scopus 로고    scopus 로고
    • The closest BLAST hit is often not the nearest neighbor
    • Koski LB, Golding GB. The closest BLAST hit is often not the nearest neighbor. J Mol Evol. 2001;52:540-2.
    • (2001) J Mol Evol , vol.52 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 11
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008;9:R151.
    • (2008) Genome Biol , vol.9 , pp. R151
    • Wu, M.1    Eisen, J.A.2
  • 15
    • 77958610660 scopus 로고    scopus 로고
    • pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics. 2010;11:538.
    • (2010) BMC Bioinformatics , vol.11 , pp. 538
    • Matsen, F.A.1    Kodner, R.B.2    Armbrust, E.V.3
  • 16
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2--approximately maximum-likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.
    • (2010) PLoS One , vol.5 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 17
    • 79961139783 scopus 로고    scopus 로고
    • Classifying short genomic fragments from novel lineages using composition and homology
    • Parks DH, MacDonald NJ, Beiko RG. Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics. 2011;12:328.
    • (2011) BMC Bioinformatics , vol.12 , pp. 328
    • Parks, D.H.1    MacDonald, N.J.2    Beiko, R.G.3
  • 18
    • 84899824262 scopus 로고    scopus 로고
    • MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences
    • Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res. 2014;42:e73.
    • (2014) Nucleic Acids Res , vol.42 , pp. e73
    • Luo, C.1    Rodriguez-R, L.M.2    Konstantinidis, K.T.3
  • 19
    • 84925243945 scopus 로고    scopus 로고
    • Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods
    • Dröge J, Gregor I, McHardy AC. Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. Bioinformatics. 2015;31:817-24.
    • (2015) Bioinformatics , vol.31 , pp. 817-824
    • Dröge, J.1    Gregor, I.2    McHardy, A.C.3
  • 20
    • 84899090573 scopus 로고    scopus 로고
    • Kraken: ultrafast metagenomic sequence classification using exact alignments
    • Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:R46.
    • (2014) Genome Biol , vol.15 , pp. R46
    • Wood, D.E.1    Salzberg, S.L.2
  • 21
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28:27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 22
    • 84891804612 scopus 로고    scopus 로고
    • The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
    • Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42(Database issue):D206-14.
    • (2014) Nucleic Acids Res , vol.42 , Issue.DATABASE ISSUE , pp. D206-D214
    • Overbeek, R.1    Olson, R.2    Pusch, G.D.3    Olsen, G.J.4    Davis, J.J.5    Disz, T.6
  • 24
    • 84879121025 scopus 로고    scopus 로고
    • MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
    • Konwar KM, Hanson NW, Pagé AP, Hallam SJ. MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. BMC Bioinformatics. 2013;14:202.
    • (2013) BMC Bioinformatics , vol.14 , pp. 202
    • Konwar, K.M.1    Hanson, N.W.2    Pagé, A.P.3    Hallam, S.J.4
  • 25
    • 84921613578 scopus 로고    scopus 로고
    • Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production
    • Doxey AC, Kurtz DA, Lynch MD, Sauder LA, Neufeld JD. Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production. ISME J. 2015;9:461-71.
    • (2015) ISME J , vol.9 , pp. 461-471
    • Doxey, A.C.1    Kurtz, D.A.2    Lynch, M.D.3    Sauder, L.A.4    Neufeld, J.D.5
  • 28
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14:755-63.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 29
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460-1.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 31
    • 34249794257 scopus 로고    scopus 로고
    • Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
    • Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007;4:495-500.
    • (2007) Nat Methods , vol.4 , pp. 495-500
    • Mavromatis, K.1    Ivanova, N.2    Barry, K.3    Shapiro, H.4    Goltsman, E.5    McHardy, A.C.6
  • 32
    • 84885819796 scopus 로고    scopus 로고
    • Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups
    • Wu D, Jospin G, Eisen JA. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One. 2013;8:e77033.
    • (2013) PLoS One , vol.8 , pp. e77033
    • Wu, D.1    Jospin, G.2    Eisen, J.A.3
  • 33
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.M.5    Kubal, M.6
  • 35
    • 79960713932 scopus 로고    scopus 로고
    • Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
    • Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4.
    • (2011) BMC Genomics , vol.12 , pp. S4
    • Liu, B.1    Gibbons, T.2    Ghodsi, M.3    Treangen, T.4    Pop, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.