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Volumn 31, Issue 12, 2015, Pages i35-i43

Reconstructing 16S rRNA genes in metagenomic data

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 16S;

EID: 84931076912     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv231     Document Type: Conference Paper
Times cited : (111)

References (40)
  • 1
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul S.F., et al. (1990). Basic local alignment search tool. J. Mol. Biol., 215, 403-410
    • (1990) J. Mol. Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 2
  • 3
    • 0030297089 scopus 로고    scopus 로고
    • The indigenous gastrointestinal microflora
    • Berg R.D. (1996). The indigenous gastrointestinal microflora. Trends Microbiol., 4, 430-435
    • (1996) Trends Microbiol , vol.4 , pp. 430-435
    • Berg, R.D.1
  • 4
    • 43149086380 scopus 로고    scopus 로고
    • Allpaths: De novo assembly of whole-genome shotgun microreads
    • Butler J., et al. (2008). ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810-820
    • (2008) Genome Res , vol.18 , pp. 810-820
    • Butler, J.1
  • 5
    • 66249131497 scopus 로고    scopus 로고
    • Global sequencing: A review of current molecular data and new methods available to assess microbial diversity
    • Christen R. (2008). Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes Environ. JSME, 23, 253-268
    • (2008) Microbes Environ. JSME , vol.23 , pp. 253-268
    • Christen, R.1
  • 6
    • 58149194632 scopus 로고    scopus 로고
    • Petabyte-scale innovations at the European nucleotide archive
    • Cochrane G., et al. (2009). Petabyte-scale innovations at the European nucleotide archive. Nucleic Acids Res., 37, D19-D25
    • (2009) Nucleic Acids Res , vol.37 , pp. D19-D25
    • Cochrane, G.1
  • 7
    • 13444304367 scopus 로고    scopus 로고
    • The ribosomal database project (rdp-ii): Sequences and tools for high-throughput rrna analysis
    • Cole J.R., et al. (2005). The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res., 33 (Suppl. 1) , D294-D296
    • (2005) Nucleic Acids Res , vol.33 , pp. D294-D296
    • Cole, J.R.1
  • 9
    • 84863004113 scopus 로고    scopus 로고
    • Reconstruction of ribosomal RNA genes from metagenomic data
    • Fan L., et al. (2012). Reconstruction of ribosomal RNA genes from metagenomic data. PloS One, 7, e39948
    • (2012) Plos One , vol.7 , pp. e39948
    • Fan, L.1
  • 10
    • 84860523681 scopus 로고    scopus 로고
    • Readjoiner: A fast and memory efficient string graph-based sequence assembler
    • Gonnella G. and Kurtz S. (2012). Readjoiner: a fast and memory efficient string graph-based sequence assembler. BMC Bioinformatics, 13, 82
    • (2012) BMC Bioinformatics , vol.13 , pp. 82
    • Gonnella, G.1    Kurtz, S.2
  • 11
    • 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, 1141-1152
    • (2009) Genome Res , vol.19 , pp. 1141-1152
    • Hamady, M.1    Knight, R.2
  • 12
    • 80052960863 scopus 로고    scopus 로고
    • Next-generation transcriptome assembly
    • Jeffrey A.M. and Zhong W. (2011). Next-generation transcriptome assembly. Nat. Rev. Genet., 12, 671-682
    • (2011) Nat. Rev. Genet , vol.12 , pp. 671-682
    • Jeffrey, A.M.1    Zhong, W.2
  • 13
    • 65549118801 scopus 로고    scopus 로고
    • Local RNA structure alignment with incomplete sequence
    • Kolbe D.L. and Eddy S.R. (2009). Local RNA structure alignment with incomplete sequence. Bioinformatics, 25, 1236-1243
    • (2009) Bioinformatics , vol.25 , pp. 1236-1243
    • Kolbe, D.L.1    Eddy, S.R.2
  • 14
    • 0036426322 scopus 로고    scopus 로고
    • The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments
    • Konings W.N., et al. (2002). The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments. Antonie Van Leeuwenhoek, 81, 61-72
    • (2002) Antonie Van Leeuwenhoek , vol.81 , pp. 61-72
    • Konings, W.N.1
  • 15
    • 79952374428 scopus 로고    scopus 로고
    • Genovo: De novo assembly for metagenomes
    • Laserson J., et al. (2011). Genovo: de novo assembly for metagenomes. J. Comput. Biol., 18, 429-443
    • (2011) J. Comput. Biol , vol.18 , pp. 429-443
    • Laserson, J.1
  • 17
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li R., et al. (2010). De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20, 265-272
    • (2010) Genome Res , vol.20 , pp. 265-272
    • Li, R.1
  • 18
    • 0035955371 scopus 로고    scopus 로고
    • Biodiversity and ecosystem functioning: Current knowledge and future challenges
    • Loreau M., et al. (2001). Biodiversity and ecosystem functioning: current knowledge and future challenges. Science, 294, 804-808
    • (2001) Science , vol.294 , pp. 804-808
    • Loreau, M.1
  • 19
    • 84858863014 scopus 로고    scopus 로고
    • Individual genome assembly from complex community short-read metagenomic datasets
    • Luo C., et al. (2012). Individual genome assembly from complex community short-read metagenomic datasets. ISME J., 6, 898-901
    • (2012) ISME J. , vol.6 , pp. 898-901
    • Luo, C.1
  • 20
    • 79956041561 scopus 로고    scopus 로고
    • Emirge: Reconstruction of full-length ribosomal genes from microbial community short read sequencing data
    • Miller C.S., et al. (2011). EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol., 12, R44
    • (2011) Genome Biol , vol.12 , pp. R44
    • Miller, C.S.1
  • 21
    • 84867397631 scopus 로고    scopus 로고
    • Metavelvet: An extension of velvet assembler to de novo metagenome assembly from short sequence reads
    • Namiki T., et al. (2012). MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res., 40, e155-e155
    • (2012) Nucleic Acids Res , vol.40 , pp. e155-e155
    • Namiki, T.1
  • 22
    • 65549111754 scopus 로고    scopus 로고
    • Infernal 1.0: Inference of RNA alignments
    • Nawrocki E.P., et al. (2009). Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337
    • (2009) Bioinformatics , vol.25 , pp. 1335-1337
    • Nawrocki, E.P.1
  • 23
    • 79959422558 scopus 로고    scopus 로고
    • Meta-IDBA: A de novo assembler for metagenomic data
    • Peng Y., et al. (2011). Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics, 27, i94-i101
    • (2011) Bioinformatics , vol.27 , pp. i94-i101
    • Peng, Y.1
  • 24
    • 84861760530 scopus 로고    scopus 로고
    • Idba-ud: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng Y., et al. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28, 1420-1428
    • (2012) Bioinformatics , vol.28 , pp. 1420-1428
    • Peng, Y.1
  • 25
    • 0035931866 scopus 로고    scopus 로고
    • Life in extreme environments
    • Rothschild L.J. and Mancinelli R.L. (2001). Life in extreme environments. Nature, 409, 1092-1101
    • (2001) Nature , vol.409 , pp. 1092-1101
    • Rothschild, L.J.1    Mancinelli, R.L.2
  • 26
    • 52949083195 scopus 로고    scopus 로고
    • Gene-boosted assembly of a novel bacterial genome from very short reads
    • Salzberg S.L., et al. (2008). Gene-boosted assembly of a novel bacterial genome from very short reads. PLOS Comput. Biol., 4, e1000186
    • (2008) Plos Comput. Biol , vol.4 , pp. e1000186
    • Salzberg, S.L.1
  • 27
    • 0017341656 scopus 로고
    • Microbial ecology of the gastrointestinal tract
    • Savage D.C. (1977). Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol., 31, 107-133
    • (1977) Annu. Rev. Microbiol , vol.31 , pp. 107-133
    • Savage, D.C.1
  • 28
    • 84878647680 scopus 로고    scopus 로고
    • Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
    • Shakya M., et al. (2013). Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ. Microbiol., 15, 1882-1899
    • (2013) Environ. Microbiol , vol.15 , pp. 1882-1899
    • Shakya, M.1
  • 29
    • 84857838310 scopus 로고    scopus 로고
    • Efficient de novo assembly of large genomes using compressed data structures
    • Simpson J.T. and Durbin R. (2012). Efficient de novo assembly of large genomes using compressed data structures. Genome Res., 22, 549-556
    • (2012) Genome Res , vol.22 , pp. 549-556
    • Simpson, J.T.1    Durbin, R.2
  • 30
    • 66449136667 scopus 로고    scopus 로고
    • Abyss: A parallel assembler for short read sequence data
    • Simpson J.T., et al. (2009). ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123
    • (2009) Genome Res , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 31
    • 0036081078 scopus 로고    scopus 로고
    • DNA Data Bank of Japan (DDBJ) for genome scale research in life science
    • Tateno Y., et al. (2002). DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res., 30, 27-30
    • (2002) Nucleic Acids Res , vol.30 , pp. 27-30
    • Tateno, Y.1
  • 32
    • 84872152255 scopus 로고    scopus 로고
    • Metamos: A modular and open source metagenomic assembly and analysis pipeline
    • Treangen T., et al. (2013). MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol., 14, R2
    • (2013) Genome Biol , vol.14 , pp. R2
    • Treangen, T.1
  • 33
    • 20244376755 scopus 로고    scopus 로고
    • Comparative metagenomics of microbial communities
    • Tringe S.G., et al. (2005). Comparative metagenomics of microbial communities. Science, 308, 554-557
    • (2005) Science , vol.308 , pp. 554-557
    • Tringe, S.G.1
  • 34
    • 34548293679 scopus 로고    scopus 로고
    • Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q., et al. (2007). Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 73, 5261-5267
    • (2007) Appl. Environ. Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1
  • 35
    • 0001271789 scopus 로고
    • Phylogenetic structure of the prokaryotic domain: The primary kingdoms
    • Woese C.R. and Fox G.E. (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci., 74, 5088-5090
    • (1977) Proc. Natl. Acad. Sci , vol.74 , pp. 5088-5090
    • Woese, C.R.1    Fox, G.E.2
  • 36
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the domains Archaea
    • Woese C.R., et al. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U.S.A, 87, 4576-4579
    • (1990) Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U.S.A , vol.87 , pp. 4576-4579
    • Woese, C.R.1
  • 37
    • 84866468781 scopus 로고    scopus 로고
    • Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics
    • Wu Y., et al. (2012). Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Bioinformatics, 28, i363-i369
    • (2012) Bioinformatics , vol.28 , pp. i363-i369
    • Wu, Y.1
  • 38
    • 84886422310 scopus 로고    scopus 로고
    • Rna-code: A noncoding rna classification tool for short reads in ngs data lacking reference genomes
    • Yuan C. and Sun Y. (2013). RNA-CODE: A noncoding RNA classification tool for short reads in NGS data lacking reference genomes. PLoS One, 8, e77596
    • (2013) Plos One , vol.8 , pp. e77596
    • Yuan, C.1    Sun, Y.2
  • 39
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de bruijn graphs
    • Zerbino D.R. and Birney E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 40
    • 84921297659 scopus 로고    scopus 로고
    • A scalable and accurate targeted gene assembly tool (sat-assembler) for next-generation sequencing data
    • Zhang Y., et al. (2014). A scalable and accurate targeted gene assembly tool (SAT-assembler) for next-generation sequencing data. PLoS Comput. Biol., 10, e1003737
    • (2014) Plos Comput. Biol , vol.10 , pp. e1003737
    • Zhang, Y.1


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