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Volumn 12, Issue , 2011, Pages

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

Author keywords

[No Author keywords available]

Indexed keywords

ACID MINE DRAINAGE; CLASSIFICATION ALGORITHM; CLASSIFICATION METHODS; COMPUTATIONAL ANALYSIS; ENVIRONMENTAL SAMPLE; ITERATIVE REFINEMENT; PHYLOGENETIC CLASSIFICATIONS; SEQUENCE SIMILARITY;

EID: 79251560623     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-41     Document Type: Article
Times cited : (58)

References (34)
  • 2
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • 10.1126/science.284.5423.2124, 10381871
    • Doolittle WF. Phylogenetic classification and the universal tree. Science 1999, 284:2124-2129. 10.1126/science.284.5423.2124, 10381871.
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 3
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 7057:376-380.
    • (2005) Nature , vol.7057 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4    Bader, J.S.5
  • 4
    • 65449144325 scopus 로고    scopus 로고
    • Evaluation of next generation sequencing platforms for population targeted sequencing studies
    • 10.1186/gb-2009-10-3-r32, 2691003, 19327155
    • Harismendy O, Ng P, Strausberg R, Wang X, Stockwell T. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 2009, 10:R32. 10.1186/gb-2009-10-3-r32, 2691003, 19327155.
    • (2009) Genome Biol , vol.10
    • Harismendy, O.1    Ng, P.2    Strausberg, R.3    Wang, X.4    Stockwell, T.5
  • 5
    • 48749117454 scopus 로고    scopus 로고
    • Species richness in soil bacterial communities: a proposed approach to overcome sample size bias
    • Youssef NH, Elshahed MS. Species richness in soil bacterial communities: a proposed approach to overcome sample size bias. J of Microb Meth 2008, 75:86-91.
    • (2008) J of Microb Meth , vol.75 , pp. 86-91
    • Youssef, N.H.1    Elshahed, M.S.2
  • 6
    • 33644692952 scopus 로고    scopus 로고
    • Metagenomics: DNA sequencing of environmental samples
    • Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples. Nature Review Genetics 2005, 6:805.
    • (2005) Nature Review Genetics , vol.6 , pp. 805
    • Tringe, S.G.1    Rubin, E.M.2
  • 7
    • 34147182303 scopus 로고    scopus 로고
    • A detailed analysis of 16 s ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
    • 10.1016/j.mimet.2007.02.005, 2562909, 17391789
    • Chakravorty S, Helb D, Burday M. A detailed analysis of 16 s ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 2007, 69(2):330-9. 10.1016/j.mimet.2007.02.005, 2562909, 17391789.
    • (2007) J Microbiol Methods , vol.69 , Issue.2 , pp. 330-339
    • Chakravorty, S.1    Helb, D.2    Burday, M.3
  • 8
    • 33644700003 scopus 로고    scopus 로고
    • Toward automatic reconstruction of a highly resolved tree of life
    • 10.1126/science.1123061, 16513982
    • Ciccarelli FD, Doerks T, von Mering C. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311(5765):1283-7. 10.1126/science.1123061, 16513982.
    • (2006) Science , vol.311 , Issue.5765 , pp. 1283-1287
    • Ciccarelli, F.D.1    Doerks, T.2    von Mering, C.3
  • 9
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • 10.1186/gb-2008-9-10-r151, 2760878, 18851752
    • Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008, 9(10):R151. 10.1186/gb-2008-9-10-r151, 2760878, 18851752.
    • (2008) Genome Biol , vol.9 , Issue.10
    • Wu, M.1    Eisen, J.A.2
  • 10
    • 77955179934 scopus 로고    scopus 로고
    • MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
    • 10.1186/1471-2164-11-461, 20687950
    • Stark M, Berger SA, Stamatakis A, von Mering C. MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics 2010, 11:461. 10.1186/1471-2164-11-461, 20687950.
    • (2010) BMC Genomics , vol.11 , pp. 461
    • Stark, M.1    Berger, S.A.2    Stamatakis, A.3    von Mering, C.4
  • 11
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • 10.1101/gr.5969107, 1800929, 17255551
    • Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007, 17:377-386. 10.1101/gr.5969107, 1800929, 17255551.
    • (2007) Genome Res , vol.17 , pp. 377-386
    • Huson, D.H.1    Auch, A.F.2    Qi, J.3    Schuster, S.C.4
  • 12
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search program
    • Altschul SF. Gapped BLAST and PSI-BLAST: a new generation of protein database search program. Nucleic Acids Res 1997, 125:3389-3402.
    • (1997) Nucleic Acids Res , vol.125 , pp. 3389-3402
    • Altschul, S.F.1
  • 13
    • 42449162998 scopus 로고    scopus 로고
    • Phylogenetic classification of short environmental DNA fragments
    • 10.1093/nar/gkn038, 2367736, 18285365
    • Krause L. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 2008, 36:2230-2239. 10.1093/nar/gkn038, 2367736, 18285365.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2230-2239
    • Krause, L.1
  • 14
    • 40149098974 scopus 로고    scopus 로고
    • Microbial ecology of four coral atolls in the Northern Line Islands
    • 10.1371/journal.pone.0001584, 2253183, 18301735
    • Dinsdale EA. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One 2008, 3:e1584. 10.1371/journal.pone.0001584, 2253183, 18301735.
    • (2008) PLoS One , vol.3
    • Dinsdale, E.A.1
  • 15
    • 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
    • 10.1186/1471-2105-5-163, 529438, 15507136
    • Teeling H, Waldmann J, Lombardot T, Bauer M, Glockner 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. 10.1186/1471-2105-5-163, 529438, 15507136.
    • (2004) BMC Bioinformatics , vol.5 , pp. 163
    • Teeling, H.1    Waldmann, J.2    Lombardot, T.3    Bauer, M.4    Glockner, F.O.5
  • 16
    • 33646569088 scopus 로고    scopus 로고
    • Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples
    • 10.1093/dnares/dsi015, 16769690
    • 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 2005, 12:281-290. 10.1093/dnares/dsi015, 16769690.
    • (2005) DNA Res , vol.12 , pp. 281-290
    • Abe, T.1    Sugawara, H.2    Kinouchi, M.3    Kanaya, S.4    Ikemura, T.5
  • 17
    • 34249081408 scopus 로고    scopus 로고
    • A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes
    • Abe T, Sugawara M, Kanaya S, Ikemura T. A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes. Polar Biosci 2006, 20:103-112.
    • (2006) Polar Biosci , vol.20 , pp. 103-112
    • Abe, T.1    Sugawara, M.2    Kanaya, S.3    Ikemura, T.4
  • 18
    • 38649143159 scopus 로고    scopus 로고
    • Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing
    • 513701:10
    • Chan CKK, Hsu AL, L TS, K HS. Using Growing Self-Organising Maps to Improve the Binning Process in Environmental Whole-Genome Shotgun Sequencing. Journal of Biomedicine and Biotechnology 2008, 513701:10.
    • (2008) Journal of Biomedicine and Biotechnology
    • Chan, C.K.K.1    Hsu, A.L.2    L, T.S.3    K, H.S.4
  • 19
    • 43749109829 scopus 로고    scopus 로고
    • Binning sequences using very sparse labels within a metagenome
    • 10.1186/1471-2105-9-215, 2383919, 18442374
    • Chan C, Hsu A, Halgamuge S, Tang S. Binning sequences using very sparse labels within a metagenome. BMC Bioinformatics 2008, 9:215. 10.1186/1471-2105-9-215, 2383919, 18442374.
    • (2008) BMC Bioinformatics , vol.9 , pp. 215
    • Chan, C.1    Hsu, A.2    Halgamuge, S.3    Tang, S.4
  • 20
    • 0034887748 scopus 로고    scopus 로고
    • Capturing whole-genome characteristics in short sequences using a naive Bayesian Classifier
    • 10.1101/gr.186401, 311094, 11483581
    • Sandberg R, Winberg G, Branden CI, Kaske A, Ernberg I, Coster J. Capturing whole-genome characteristics in short sequences using a naive Bayesian Classifier. Genome Research 2001, 11:1404-1409. 10.1101/gr.186401, 311094, 11483581.
    • (2001) Genome Research , vol.11 , pp. 1404-1409
    • Sandberg, R.1    Winberg, G.2    Branden, C.I.3    Kaske, A.4    Ernberg, I.5    Coster, J.6
  • 21
    • 33644872947 scopus 로고    scopus 로고
    • Bayesian Classifiers for detecting HGT using xed and variable order Markov models of genomic signatures
    • Dalevi D, Dubashi D, Hermansson M. Bayesian Classifiers for detecting HGT using xed and variable order Markov models of genomic signatures. Bioinformatics March 2006, 22:517-522.
    • (2006) Bioinformatics March , vol.22 , pp. 517-522
    • Dalevi, D.1    Dubashi, D.2    Hermansson, M.3
  • 22
    • 33845957530 scopus 로고    scopus 로고
    • Accurate phylogenetic classification of variable-length DNA fragments
    • 10.1038/nmeth976, 17179938
    • McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 2007, 4:63-72. 10.1038/nmeth976, 17179938.
    • (2007) Nat Methods , vol.4 , pp. 63-72
    • McHardy, A.C.1    Martin, H.G.2    Tsirigos, A.3    Hugenholtz, P.4    Rigoutsos, I.5
  • 23
    • 62549109116 scopus 로고    scopus 로고
    • TTACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    • 10.1186/1471-2105-10-56, 2653487, 19210774
    • Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW. TTACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics 2009, 10:56. 10.1186/1471-2105-10-56, 2653487, 19210774.
    • (2009) BMC Bioinformatics , vol.10 , pp. 56
    • Diaz, N.N.1    Krause, L.2    Goesmann, A.3    Niehaus, K.4    Nattkemper, T.W.5
  • 24
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • 10.1038/nmeth.1358, 2762791, 19648916
    • Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 2009, 6:673-676. 10.1038/nmeth.1358, 2762791, 19648916.
    • (2009) Nat Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 26
    • 1242335920 scopus 로고    scopus 로고
    • Whole proteome prokaryote phylogeny without sequence alignment: A k-string composition approach
    • Qi J, Wang B, Hao BI. Whole proteome prokaryote phylogeny without sequence alignment: A k-string composition approach. ournal of Molecular Evolution 2004, 58:1-11.
    • (2004) ournal of Molecular Evolution , vol.58 , pp. 1-11
    • Qi, J.1    Wang, B.2    Hao, B.I.3
  • 27
    • 34548805887 scopus 로고    scopus 로고
    • A quantitative genotype algorithm reffectin H5N1 avian in uenza niches
    • 10.1093/bioinformatics/btm354, 17623701
    • Wan CG X F, Luo F, Emch M, Donis R. A quantitative genotype algorithm reffectin H5N1 avian in uenza niches. Bioinformatics 2007, 23:2368-2375. 10.1093/bioinformatics/btm354, 17623701.
    • (2007) Bioinformatics , vol.23 , pp. 2368-2375
    • Wan CG X, F.1    Luo, F.2    Emch, M.3    Donis, R.4
  • 30
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Database, 10.1093/nar/gkl842, 1716718, 17130148
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, (35 Database):D61-D65. 10.1093/nar/gkl842, 1716718, 17130148.
    • (2007) Nucleic Acids Res , Issue.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 31
    • 62449130191 scopus 로고    scopus 로고
    • Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
    • Sims GE, Jun SR, Wu GA, Kim SH. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci US 2008, 106:2677-2682.
    • (2008) Proc Natl Acad Sci US , vol.106 , pp. 2677-2682
    • Sims, G.E.1    Jun, S.R.2    Wu, G.A.3    Kim, S.H.4
  • 32
    • 0033931867 scopus 로고    scopus 로고
    • Assessing the accuracy of prediction algorithms for classification: an overview
    • 10.1093/bioinformatics/16.5.412, 10871264
    • Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16:412-424. 10.1093/bioinformatics/16.5.412, 10871264.
    • (2000) Bioinformatics , vol.16 , pp. 412-424
    • Baldi, P.1    Brunak, S.2    Chauvin, Y.3    Andersen, C.A.4    Nielsen, H.5
  • 33
    • 1542377296 scopus 로고    scopus 로고
    • Community structure and metabolism through reconstruction of microbial genomes from the environment
    • 10.1038/nature02340, 14961025
    • Tyson GW. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428:37-43. 10.1038/nature02340, 14961025.
    • (2004) Nature , vol.428 , pp. 37-43
    • Tyson, G.W.1


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