메뉴 건너뛰기




Volumn 19, Issue 2, 2012, Pages 241-249

MetaCluster 4.0: A novel binning algorithm for NGS reads and huge number of species

Author keywords

binning; environmental genomics; metagenomics

Indexed keywords

ALGORITHM; BACTERIAL GENOME; BACTERIUM; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONFERENCE PAPER; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; NUCLEOTIDE SEQUENCE; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 84863049441     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0276     Document Type: Conference Paper
Times cited : (57)

References (26)
  • 1
    • 0025294528 scopus 로고
    • Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations
    • Amann, R.I., Binder, B.J., Olson, R.J., et al. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919.
    • (1990) Appl. Environ. Microbiol , vol.56 , pp. 1919
    • Amann, R.I.1    Binder, B.J.2    Olson, R.J.3
  • 2
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models
    • Brady, A., and Salzberg, S.L. 2009. Phymm and PhymmBL: metagenomic phylogenetic 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
    • 33846131262 scopus 로고    scopus 로고
    • Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies
    • Case, R.J., Boucher, Y., Dahllof, I., et al. 2007. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl. Environ. Microbiol. 73, 278.
    • (2007) Appl. Environ. Microbiol , vol.73 , pp. 278
    • Case, R.J.1    Boucher, Y.2    Dahllof, I.3
  • 4
    • 47249139915 scopus 로고    scopus 로고
    • CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads
    • Chatterji, S., Yamazaki, I., Bai, Z., et al. 2008. CompostBin: a DNA composition-based algorithm for binning environmental shotgun reads. Lect. Notes Bioinform. 4955, 17-28.
    • (2008) Lect. Notes Bioinform , vol.4955 , pp. 17-28
    • Chatterji, S.1    Yamazaki, I.2    Bai, Z.3
  • 5
    • 13444304367 scopus 로고    scopus 로고
    • The Ribosomal Database Project (RDP-II): Sequences and tools for highthroughput rRNA analysis
    • Cole, J., Chai, B., Farris, R., et al. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for highthroughput rRNA analysis. Nucleic Acids Res. 33, D294.
    • (2005) Nucleic Acids Res , vol.33
    • Cole, J.1    Chai, B.2    Farris, R.3
  • 6
    • 72949091232 scopus 로고    scopus 로고
    • Bacterial community variation in human body habitats across space and time
    • Costello, E.K., Lauber, C.L., Hamady, M., et al. 2009. Bacterial community variation in human body habitats across space and time. Science 326, 1694.
    • (2009) Science , vol.326 , pp. 1694
    • Costello, E.K.1    Lauber, C.L.2    Hamady, M.3
  • 7
    • 33947221422 scopus 로고    scopus 로고
    • Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes
    • Eisen, J.A. 2007. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol. 5, e82.
    • (2007) PLoS Biol , vol.5
    • Eisen, J.A.1
  • 9
    • 66349083859 scopus 로고    scopus 로고
    • Topographical and temporal diversity of the human skin microbiome
    • Grice, E.A., Kong, H.H., Conlan, S., et al. 2009. Topographical and temporal diversity of the human skin microbiome. Science 324, 1190.
    • (2009) Science , vol.324 , pp. 1190
    • Grice, E.A.1    Kong, H.H.2    Conlan, S.3
  • 10
    • 67650021209 scopus 로고    scopus 로고
    • Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
    • Hamady, M., and Knight, R. 2009. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 19, 1141.
    • (2009) Genome Res , vol.19 , pp. 1141
    • Hamady, M.1    Knight, R.2
  • 11
    • 77958605377 scopus 로고    scopus 로고
    • Clustering metagenomic sequences with interpolated Markov models
    • Kelley, D.R., and Salzberg, S.L. 2010. Clustering metagenomic sequences with interpolated Markov models. BMC Bioinform. 11, 544.
    • (2010) BMC Bioinform. , vol.11 , pp. 544
    • Kelley, D.R.1    Salzberg, S.L.2
  • 12
    • 51849086745 scopus 로고    scopus 로고
    • Predominant role of host genetics in controlling the composition of gut microbiota
    • Khachatryan, Z.A., Ktsoyan, Z.A., Manukyan, G.P., et al. 2008. Predominant role of host genetics in controlling the composition of gut microbiota. PLoS ONE 3, e3064.
    • (2008) PLoS ONE , vol.3
    • Khachatryan, Z.A.1    Ktsoyan, Z.A.2    Manukyan, G.P.3
  • 13
    • 0034992826 scopus 로고    scopus 로고
    • The closest BLAST hit is often not the nearest neighbor
    • Koski, L.B., and Golding, G.B. 2001. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52, 540-542. (Pubitemid 32507075)
    • (2001) Journal of Molecular Evolution , vol.52 , Issue.6 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 14
    • 79957877228 scopus 로고    scopus 로고
    • A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio
    • Leung, H., Yiu, S., Yang, B., et al. 2011. A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio. Bioinformatics 27, 1489.
    • (2011) Bioinformatics , vol.27 , pp. 1489
    • Leung, H.1    Yiu, S.2    Yang, B.3
  • 15
    • 33845957530 scopus 로고    scopus 로고
    • Accurate phylogenetic classification of variable-length DNA fragments
    • McHardy, A.C., Mart́n, H.G., Tsirigos, A., et al. 2006. Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods 4, 63-72.
    • (2006) Nat. Methods , vol.4 , pp. 63-72
    • McHardy, A.C.1    Mart́n, H.G.2    Tsirigos, A.3
  • 16
    • 67650456399 scopus 로고    scopus 로고
    • Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information
    • Navlakha, S., White, J., Nagarajan, N., et al. 2009. Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Lect. Notes Comput. Sci. 5541, 400-417.
    • (2009) Lect. Notes Comput. Sci , vol.5541 , pp. 400-417
    • Navlakha, S.1    White, J.2    Nagarajan, N.3
  • 18
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin, J., Li, R., Raes, J., et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65.
    • (2010) Nature , vol.464 , pp. 59-65
    • Qin, J.1    Li, R.2    Raes, J.3
  • 19
    • 33947238287 scopus 로고    scopus 로고
    • The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific
    • Rusch, D.B., Halpern, A.L., Sutton, G., et al. 2007. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5, e77.
    • (2007) PLoS Biol , vol.5
    • Rusch, D.B.1    Halpern, A.L.2    Sutton, G.3
  • 20
    • 4344670204 scopus 로고    scopus 로고
    • Application of tetranucleotide frequencies for the assignment of genomic fragments
    • DOI 10.1111/j.1462-2920.2004.00624.x
    • Teeling, H., Meyerdierks, A., Bauer, M., et al. 2004a. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ. Microbiol. 6, 938-947. (Pubitemid 39123248)
    • (2004) Environmental Microbiology , vol.6 , Issue.9 , pp. 938-947
    • Teeling, H.1    Meyerdierks, A.2    Bauer, M.3    Amann, R.4    Glockner, F.O.5
  • 21
    • 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., et al. 2004b. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinform. 5, 163.
    • (2004) BMC Bioinform , vol.5 , pp. 163
    • Teeling, H.1    Waldmann, J.2    Lombardot, T.3
  • 23
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu, M., and Eisen, J.A. 2008. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9, 1-11.
    • (2008) Genome Biol , vol.9 , pp. 1-11
    • Wu, M.1    Eisen, J.A.2
  • 24
    • 79952425617 scopus 로고    scopus 로고
    • A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
    • Wu, Y.W., and Ye, Y. 2011. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J. Comput. Biol. 18, 523-534.
    • (2011) J. Comput. Biol. , vol.18 , pp. 523-534
    • Wu, Y.W.1    Ye, Y.2
  • 25
    • 77958056824 scopus 로고    scopus 로고
    • MetaCluster: Unsupervised binning of environmental genomic fragments and taxonomic annotation
    • Yang, B., Peng, Y., Leung, H., et al. 2010a. MetaCluster: unsupervised binning of environmental genomic fragments and taxonomic annotation. Proc. First ACM Int. Conf. Bioinform. Comput. Biol. 170-179.
    • (2010) Proc. First. ACM Int. Conf. Bioinform. Comput. Biol. , pp. 170-179
    • Yang, B.1    Peng, Y.2    Leung, H.3
  • 26
    • 77952894198 scopus 로고    scopus 로고
    • Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers
    • Yang, B., Peng, Y., Leung, H., et al. 2010b. Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. BMC Bioinform. 11, S5.
    • (2010) BMC Bioinform , vol.11
    • Yang, B.1    Peng, Y.2    Leung, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.