메뉴 건너뛰기




Volumn 15, Issue 6, 2015, Pages 1403-1414

metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

Author keywords

16S; 18S; Metagenomics; Microbial communities; rRNA libraries; Taxonomic assignment

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA; RNA 16S; RNA 18S; RNA 23S; RNA, RIBOSOMAL, 26S;

EID: 84943580979     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12399     Document Type: Article
Times cited : (324)

References (39)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schäffer AA et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
    • (1997) Nucleic Acids Research , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3
  • 2
    • 80054117496 scopus 로고    scopus 로고
    • Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets
    • Bengtsson J, Eriksson KM, Hartmann M et al. (2011) Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek, 100, 471-475.
    • (2011) Antonie van Leeuwenhoek , vol.100 , pp. 471-475
    • Bengtsson, J.1    Eriksson, K.M.2    Hartmann, M.3
  • 3
    • 84865596022 scopus 로고    scopus 로고
    • Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets
    • Bengtsson J, Hartmann M, Unterseher M et al. (2012) Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets. Research in Microbiology, 163, 407-412.
    • (2012) Research in Microbiology , vol.163 , pp. 407-412
    • Bengtsson, J.1    Hartmann, M.2    Unterseher, M.3
  • 5
    • 84885611996 scopus 로고    scopus 로고
    • Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
    • Bengtsson-Palme J, Ryberg M, Hartmann M et al. (2013b) Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution, 4, 914-919.
    • (2013) Methods in Ecology and Evolution , vol.4 , pp. 914-919
    • Bengtsson-Palme, J.1    Ryberg, M.2    Hartmann, M.3
  • 7
    • 2942571539 scopus 로고    scopus 로고
    • The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    • Cannone JJ, Subramanian S, Schnare MN et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.
    • (2002) BMC Bioinformatics , vol.3 , pp. 2
    • Cannone, J.J.1    Subramanian, S.2    Schnare, M.N.3
  • 8
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high-throughput community sequencing data
    • Caporaso JG, Kuczynski J, Stombaugh J et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
    • (2010) Nature Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1    Kuczynski, J.2    Stombaugh, J.3
  • 9
    • 33746061683 scopus 로고    scopus 로고
    • Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
    • DeSantis TZ, Hugenholtz P, Larsen N et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72, 5069-5072.
    • (2006) Applied and Environmental Microbiology , vol.72 , pp. 5069-5072
    • DeSantis, T.Z.1    Hugenholtz, P.2    Larsen, N.3
  • 10
    • 84862177773 scopus 로고    scopus 로고
    • MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa
    • D'Onorio de Meo P, D'Antonio M, Griggio F et al. (2012) MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa. Nucleic Acids Research, 40, D1168-D1172.
    • (2012) Nucleic Acids Research , vol.40 , pp. D1168-D1172
    • D'Onorio de Meo, P.1    D'Antonio, M.2    Griggio, F.3
  • 11
    • 84881564427 scopus 로고    scopus 로고
    • Bacterial communities associated with culex mosquito larvae and two emergent aquatic plants of bioremediation importance
    • Duguma D, Rugman-Jones P, Kaufman MG et al. (2013) Bacterial communities associated with culex mosquito larvae and two emergent aquatic plants of bioremediation importance. PLoS ONE, 8, e72522.
    • (2013) PLoS ONE , vol.8 , pp. e72522
    • Duguma, D.1    Rugman-Jones, P.2    Kaufman, M.G.3
  • 12
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy SR (2011) Accelerated profile HMM searches. PLoS Computational Biology, 7, e1002195.
    • (2011) PLoS Computational Biology , vol.7 , pp. e1002195
    • Eddy, S.R.1
  • 13
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 14
    • 84889649570 scopus 로고    scopus 로고
    • Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data
    • Eren AM, Maignien L, Sul WJ et al. (2013) Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods in Ecology and Evolution, 4, 1111-1119.
    • (2013) Methods in Ecology and Evolution , vol.4 , pp. 1111-1119
    • Eren, A.M.1    Maignien, L.2    Sul, W.J.3
  • 15
    • 84863004113 scopus 로고    scopus 로고
    • Reconstruction of ribosomal RNA genes from metagenomic data
    • Fan L, McElroy K, Thomas T (2012) Reconstruction of ribosomal RNA genes from metagenomic data. PLoS ONE, 7, e39948.
    • (2012) PLoS ONE , vol.7 , pp. e39948
    • Fan, L.1    McElroy, K.2    Thomas, T.3
  • 16
    • 33845986334 scopus 로고    scopus 로고
    • Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA
    • Freyhult EK, Bollback JP, Gardner PP (2007) Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research, 17, 117-125.
    • (2007) Genome Research , vol.17 , pp. 117-125
    • Freyhult, E.K.1    Bollback, J.P.2    Gardner, P.P.3
  • 18
    • 84901336727 scopus 로고    scopus 로고
    • Human and environmental impacts on river sediment microbial communities
    • Gibbons SM, Jones E, Bearquiver A et al. (2014) Human and environmental impacts on river sediment microbial communities. PLoS ONE, 9, e97435.
    • (2014) PLoS ONE , vol.9 , pp. e97435
    • Gibbons, S.M.1    Jones, E.2    Bearquiver, A.3
  • 19
    • 77957860163 scopus 로고    scopus 로고
    • V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences
    • Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH (2010) V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. Journal of Microbiological Methods, 83, 250-253.
    • (2010) Journal of Microbiological Methods , vol.83 , pp. 250-253
    • Hartmann, M.1    Howes, C.G.2    Abarenkov, K.3    Mohn, W.W.4    Nilsson, R.H.5
  • 20
    • 84860162730 scopus 로고    scopus 로고
    • Introduction to the analysis of environmental sequences: metagenomics with MEGAN
    • Huson DH, Mitra S (2012) Introduction to the analysis of environmental sequences: metagenomics with MEGAN. Methods in Molecular Biology, 856, 415-429.
    • (2012) Methods in Molecular Biology , vol.856 , pp. 415-429
    • Huson, D.H.1    Mitra, S.2
  • 21
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9, 286-298.
    • (2008) Briefings in Bioinformatics , vol.9 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 22
    • 84876786639 scopus 로고    scopus 로고
    • Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest
    • Kerekes J, Kaspari M, Stevenson B et al. (2013) Nutrient enrichment increased species richness of leaf litter fungal assemblages in a tropical forest. Molecular Ecology, 22, 2827-2838.
    • (2013) Molecular Ecology , vol.22 , pp. 2827-2838
    • Kerekes, J.1    Kaspari, M.2    Stevenson, B.3
  • 23
    • 84860756398 scopus 로고    scopus 로고
    • Performance comparison of benchtop high-throughput sequencing platforms
    • Loman NJ, Misra RV, Dallman TJ et al. (2012) Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30, 434-439.
    • (2012) Nature Biotechnology , vol.30 , pp. 434-439
    • Loman, N.J.1    Misra, R.V.2    Dallman, T.J.3
  • 24
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald D, Price MN, Goodrich J et al. (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME Journal, 6, 610-618.
    • (2012) The ISME Journal , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.N.2    Goodrich, J.3
  • 25
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, Dsouza M et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics, 9, 386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    Dsouza, M.3
  • 26
    • 84872132821 scopus 로고    scopus 로고
    • Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs
    • Mizrahi-Man O, Davenport ER, Gilad Y (2013) Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS ONE, 8, e53608.
    • (2013) PLoS ONE , vol.8 , pp. e53608
    • Mizrahi-Man, O.1    Davenport, E.R.2    Gilad, Y.3
  • 28
    • 84865060813 scopus 로고    scopus 로고
    • PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets
    • Pinto AJ, Raskin L (2012) PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE, 7, e43093.
    • (2012) PLoS ONE , vol.7 , pp. e43093
    • Pinto, A.J.1    Raskin, L.2
  • 29
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
    • Quast C, Pruesse E, Yilmaz P et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41, D590-D596.
    • (2013) Nucleic Acids Research , vol.41 , pp. D590-D596
    • Quast, C.1    Pruesse, E.2    Yilmaz, P.3
  • 30
  • 31
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: the European molecular biology open software suite
    • Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends in Genetics: TIG, 16, 276-277.
    • (2000) Trends in Genetics: TIG , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 32
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
    • Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537-7541.
    • (2009) Applied and Environmental Microbiology , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3
  • 34
    • 84862631902 scopus 로고    scopus 로고
    • Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
    • Soergel DAW, Dey N, Knight R, Brenner SE (2012) Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. The ISME Journal, 6, 1440-1444.
    • (2012) The ISME Journal , vol.6 , pp. 1440-1444
    • Soergel, D.A.W.1    Dey, N.2    Knight, R.3    Brenner, S.E.4
  • 35
    • 33847343531 scopus 로고    scopus 로고
    • An evaluation of LSU rDNA D1-D2 sequences for their use in species identification
    • Sonnenberg R, Nolte AW, Tautz D (2007) An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Frontiers in Zoology, 4, 6.
    • (2007) Frontiers in Zoology , vol.4 , pp. 6
    • Sonnenberg, R.1    Nolte, A.W.2    Tautz, D.3
  • 37
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73, 5261-5267.
    • (2007) Applied and Environmental Microbiology , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 38
    • 84899632740 scopus 로고    scopus 로고
    • Importance of saprotrophic freshwater fungi for pollen degradation
    • Wurzbacher C, Rösel S, Rychła A, Grossart H-P (2014) Importance of saprotrophic freshwater fungi for pollen degradation. PLoS ONE, 9, e94643.
    • (2014) PLoS ONE , vol.9 , pp. e94643
    • Wurzbacher, C.1    Rösel, S.2    Rychła, A.3    Grossart, H.-P.4
  • 39
    • 84859588806 scopus 로고    scopus 로고
    • The future of environmental DNA in ecology
    • Yoccoz NG (2012) The future of environmental DNA in ecology. Molecular Ecology, 21, 2031-2038.
    • (2012) Molecular Ecology , vol.21 , pp. 2031-2038
    • Yoccoz, N.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.