메뉴 건너뛰기




Volumn 29, Issue 15, 2013, Pages 1858-1864

SPANNER: Taxonomic assignment of sequences using pyramid matching of similarity profiles

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; GENOMICS; METAGENOME; METHODOLOGY; MICROBIAL GENOME; PHYLOGENY; SEQUENCE ALIGNMENT; PROCEDURES;

EID: 84880548573     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt313     Document Type: Article
Times cited : (8)

References (16)
  • 2
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: Metagenomic phylogen-etic classification with interpolated Markov models
    • Brady, A. and Salzberg, S.L. (2009) Phymm and PhymmBL: metagenomic phylogen-etic classification with interpolated Markov models. Nat. Methods, 6, 673-676.
    • (2009) Nat. Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 3
    • 4544353362 scopus 로고    scopus 로고
    • Accelerated bioremediation of trichloroethene: From field and laboratory studies to full scale
    • Batelle Press, Monterey, CA
    • Cox, E.E. et al. (1998) Accelerated bioremediation of trichloroethene: from field and laboratory studies to full scale. In: Remediation of Chlorinated and Recalcitrant Compounds. Batelle Press, Monterey, CA.
    • (1998) Remediation of Chlorinated and Recalcitrant Compounds
    • Cox, E.E.1
  • 4
    • 62549109116 scopus 로고    scopus 로고
    • TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    • Diaz, N.N. et al. (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
  • 5
    • 33751020235 scopus 로고    scopus 로고
    • Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides
    • DOI 10.1111/j.1574-6941.2006.00191.x
    • Duhamel, M. and Edwards, E.A. (2006) Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. FEMS Microbiol. Ecol., 58, 538-549. (Pubitemid 44748161)
    • (2006) FEMS Microbiology Ecology , vol.58 , Issue.3 , pp. 538-549
    • Duhamel, M.1    Edwards, E.A.2
  • 6
    • 0003437302 scopus 로고    scopus 로고
    • version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
    • Felsenstein, J. (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
    • (2005) PHYLIP (Phylogeny Inference Package)
    • Felsenstein, J.1
  • 7
    • 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
    • Gerlach, W.1    Stoye, J.2
  • 8
    • 34247576789 scopus 로고    scopus 로고
    • The pyramid match kernel: Efficient learning with sets of features
    • Grauman, K. and Darrell, T. (2007) The pyramid match kernel: efficient learning with sets of image features. J. Mach. Learn. Res., 8, 725-760. (Pubitemid 46677049)
    • (2007) Journal of Machine Learning Research , vol.8 , pp. 725-760
    • Grauman, K.1    Darrell, T.2
  • 9
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • Huson, H. et al. (2007) MEGAN analysis of metagenomic data. Genome Res., 17, 377-386.
    • (2007) Genome Res. , vol.17 , pp. 377-386
    • Huson, H.1
  • 10
    • 84864945803 scopus 로고    scopus 로고
    • Rapid identification of high-confidence taxonomic assignments for metagenomic data
    • MacDonald, N.J. et al. (2012) Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res., 40, e111.
    • (2012) Nucleic Acids Res. , vol.40
    • MacDonald, N.J.1
  • 11
    • 35748959318 scopus 로고    scopus 로고
    • What's in the mix: Phylogenetic classification of metagenome sequence samples
    • DOI 10.1016/j.mib.2007.08.004, PII S136952740700118X, Antimicrobials/Genomics
    • McHardy, A.C. and Rigoutsos, I. (2007) What's in the mix: phylogenetic classification of metagenome sequence samples. Curr. Opin. Microbiol., 10, 499-503. (Pubitemid 350052685)
    • (2007) Current Opinion in Microbiology , vol.10 , Issue.5 , pp. 499-503
    • McHardy, A.C.1    Rigoutsos, I.2
  • 12
    • 67649887316 scopus 로고    scopus 로고
    • SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
    • Monzoorul, H.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, H.M.1
  • 13
    • 79961139783 scopus 로고    scopus 로고
    • Classifying short genomic fragments from novel lineages using composition and homology
    • Parks, D. et al. (2011) Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics, 12, 328.
    • (2011) BMC Bioinformatics , vol.12 , pp. 328
    • Parks, D.1
  • 14
    • 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
  • 15
    • 77958476427 scopus 로고    scopus 로고
    • Distinguishing microbial genome fragments based on their composition: Evolutionary and comparative genomic perspectives
    • Perry, S.C. and Beiko, R.G. (2010) Distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives. Genome Biol. Evol., 2, 117-131.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 117-131
    • Perry, S.C.1    Beiko, R.G.2
  • 16
    • 77955902981 scopus 로고    scopus 로고
    • Ab initio gene identification in metagenomic sequences
    • Zhu, W. et al. (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res., 38, e132.
    • (2010) Nucleic Acids Res. , vol.38
    • Zhu, W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.