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Volumn 11, Issue 9, 2016, Pages

WEVOTE: Weighted voting taxonomic identification method of microbial sequences

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BENCHMARKING; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; DNA SEQUENCE; FALSE POSITIVE RESULT; GENOME ANALYSIS; MATHEMATICAL COMPUTING; MEASUREMENT PRECISION; METAGENOME; MICROBIAL DIVERSITY; MICROBIAL IDENTIFICATION; MICROBIAL SEQUENCE; NONHUMAN; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; TAXONOMIC IDENTIFICATION; WEIGHTED VOTING TAXONOMIC IDENTIFICATION;

EID: 84991702475     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0163527     Document Type: Article
Times cited : (22)

References (23)
  • 1
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • PMID: 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology. 2009; 10(3):R25. doi: 10.1186/gb-2009-10-3-r25 PMID: 19261174
    • (2009) Genome Biology , vol.10 , Issue.3 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 4
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models
    • PMID: 19648916
    • Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature methods. 2009; 6(9):673-6. doi: 10.1038/nmeth.1358 PMID: 19648916
    • (2009) Nature Methods , vol.6 , Issue.9 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 5
    • 84899090573 scopus 로고    scopus 로고
    • Kraken: Ultrafast metagenomic sequence classification using exact alignments
    • PMID: 24580807
    • Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome biology. 2014; 15(3):R46. doi: 10.1186/gb-2014-15-3-r46 PMID: 24580807
    • (2014) Genome Biology , vol.15 , Issue.3 , pp. R46
    • Wood, D.E.1    Salzberg, S.L.2
  • 6
    • 0034992826 scopus 로고    scopus 로고
    • The Closest BLAST Hit Is Often Not the Nearest Neighbor
    • PMID: 11443357
    • Koski LB, Golding GB. The Closest BLAST Hit Is Often Not the Nearest Neighbor. Journal of Molecular Evolution. 2001; 52(6):540-542. doi: 10.1007/s002390010184 PMID: 11443357
    • (2001) Journal of Molecular Evolution , vol.52 , Issue.6 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 7
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • PMID: 17255551
    • Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome research. 2007; 17(3):377-86. doi: 10.1101/gr.5969107 PMID: 17255551
    • (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
  • 8
    • 84922751927 scopus 로고    scopus 로고
    • TIPP: Taxonomic identification and phylogenetic profiling
    • Oxford, England
    • Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T. TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics (Oxford, England). 2014; 30(24):3548-55. doi: 10.1093/bioinformatics/btu721
    • (2014) Bioinformatics , vol.30 , Issue.24 , pp. 3548-3555
    • Nguyen, N.P.1    Mirarab, S.2    Liu, B.3    Pop, M.4    Warnow, T.5
  • 9
    • 79960869431 scopus 로고    scopus 로고
    • Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
    • PMID: 21989143
    • 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(2):S4. doi: 10.1186/1471-2164-12-S2-S4 PMID: 21989143
    • (2011) BMC Genomics , vol.12 , Issue.2 , pp. S4
    • Liu, B.1    Gibbons, T.2    Ghodsi, M.3    Treangen, T.4    Pop, M.5
  • 10
    • 84888884475 scopus 로고    scopus 로고
    • Metagenomic species profiling using universal phylogenetic marker genes
    • PMID: 24141494
    • Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, et al. Metagenomic species profiling using universal phylogenetic marker genes. Nature methods. 2013; 10(12):1196-9. doi: 10.1038/nmeth.2693 PMID: 24141494
    • (2013) Nature Methods , vol.10 , Issue.12 , pp. 1196-1199
    • Sunagawa, S.1    Mende, D.R.2    Zeller, G.3    Izquierdo-Carrasco, F.4    Berger, S.A.5    Kultima, J.R.6
  • 11
    • 84864440400 scopus 로고    scopus 로고
    • Metagenomic microbial community profiling using unique clade-specific marker genes
    • PMID: 22688413
    • Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature methods. 2012; 9(8):811-4. doi: 10.1038/nmeth.2066 PMID: 22688413
    • (2012) Nature Methods , vol.9 , Issue.8 , pp. 811-814
    • Segata, N.1    Waldron, L.2    Ballarini, A.3    Narasimhan, V.4    Jousson, O.5    Huttenhower, C.6
  • 12
  • 13
    • 84929174408 scopus 로고    scopus 로고
    • CLARK: Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
    • PMID: 25879410
    • Ounit R, Wanamaker S, Close TJ, Lonardi S. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics. 2015; 16(1):236. doi: 10.1186/s12864-015-1419-2 PMID: 25879410
    • (2015) BMC Genomics , vol.16 , Issue.1 , pp. 236
    • Ounit, R.1    Wanamaker, S.2    Close, T.J.3    Lonardi, S.4
  • 14
    • 84883468661 scopus 로고    scopus 로고
    • Scalable metagenomic taxonomy classification using a reference genome database
    • Oxford, England
    • Ames SK, Hysom DA, Gardner SN, Lloyd GS, Gokhale MB, Allen JE. Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics (Oxford, England). 2013; 29 (18):2253-60. doi: 10.1093/bioinformatics/btt389
    • (2013) Bioinformatics , vol.29 , Issue.18 , pp. 2253-2260
    • Ames, S.K.1    Hysom, D.A.2    Gardner, S.N.3    Lloyd, G.S.4    Gokhale, M.B.5    Allen, J.E.6
  • 16
    • 78650549608 scopus 로고    scopus 로고
    • NBC: The Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads
    • Oxford, England
    • Rosen GL, Reichenberger ER, Rosenfeld AM. NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics (Oxford, England). 2011; 27(1):127-9. doi: 10.1093/bioinformatics/btq619
    • (2011) Bioinformatics , vol.27 , Issue.1 , pp. 127-129
    • Rosen, G.L.1    Reichenberger, E.R.2    Rosenfeld, A.M.3
  • 17
    • 84954556725 scopus 로고    scopus 로고
    • An evaluation of the accuracy and speed of metagenome analysis tools
    • PMID: 26778510
    • Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports. 2016; 6:19233. doi: 10.1038/srep19233 PMID: 26778510
    • Scientific Reports , vol.2016 , Issue.6
    • Lindgreen, S.1    Adair, K.L.2    Gardner, P.P.3
  • 18
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • PMID: 18851752
    • Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biology. 2008; 9(10):R151. doi: 10.1186/gb-2008-9-10-r151 PMID: 18851752
    • (2008) Genome Biology , vol.9 , Issue.10 , pp. R151
    • Wu, M.1    Eisen, J.A.2
  • 19
    • 84555194934 scopus 로고    scopus 로고
    • SATe-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees
    • PMID: 22139466
    • Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, et al. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic biology. 2012; 61(1):90-106. doi: 10.1093/sysbio/syr095 PMID: 22139466
    • (2012) Systematic Biology , vol.61 , Issue.1 , pp. 90-106
    • Liu, K.1    Warnow, T.J.2    Holder, M.T.3    Nelesen, S.M.4    Yu, J.5    Stamatakis, A.P.6
  • 20
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Oxford, England
    • Eddy SR. Profile hidden Markov models. Bioinformatics (Oxford, England). 1998; 14(9):755-63. doi: 10.1093/bioinformatics/14.9.755
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 755-763
    • Eddy, S.R.1
  • 21
    • 77958610660 scopus 로고    scopus 로고
    • pplacer: Linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • PMID: 21034504
    • 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. doi: 10.1186/1471-2105-11-538 PMID: 21034504
    • (2010) BMC Bioinformatics , vol.11 , pp. 538
    • Matsen, F.A.1    Kodner, R.B.2    Armbrust, E.V.3
  • 22
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic acids research. 2010; 38(Database issue):355-60. doi: 10.1093/nar/gkp896
    • (2010) Nucleic Acids Research , vol.38 , Issue.DATABASE ISSUE , pp. 355-360
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 23
    • 79959245159 scopus 로고    scopus 로고
    • Berlin, Heidelberg: Springer Berlin Heidelberg
    • Deza E, Deza MM. Encyclopedia of Distances. Berlin, Heidelberg: Springer Berlin Heidelberg; 2009. Available from: http://link.springer.com/10.1007/978-3-642-00234-2
    • (2009) Encyclopedia of Distances
    • Deza, E.1    Deza, M.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.