메뉴 건너뛰기




Volumn 2010, Issue 6, 2010, Pages 189-196

Plutof-a web based workbench for ecological and taxonomic research, with an online implementation for fungal its sequences

Author keywords

Data mining; Metadata; Sequence identification; Sequence management environment; Thin clients

Indexed keywords

INTERNAL TRANSCRIBED SPACER;

EID: 78650578953     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S6271     Document Type: Article
Times cited : (234)

References (50)
  • 2
    • 53149135089 scopus 로고    scopus 로고
    • Fungal community ecology: A hybrid beast with a molecular master
    • Peay KG, Kennedy PG, Bruns TD. Fungal community ecology: a hybrid beast with a molecular master. BioScience. 2008;58:799-810.
    • (2008) BioScience , vol.58 , pp. 799-810
    • Peay, K.G.1    Kennedy, P.G.2    Bruns, T.D.3
  • 5
  • 6
  • 7
    • 79952428465 scopus 로고    scopus 로고
    • Rethinking taxon sampling in the light of environmental sequencing.Cladistics
    • 10.1111/j. 1096-0031.2010.00336.x (in press)
    • Nilsson RH, Ryberg M, Sjökvist E, Abarenkov K. Rethinking taxon sampling in the light of environmental sequencing. Cladistics. 2010;doi:10.1111/j. 1096-0031.2010.00336.x (in press).
    • (2010)
    • Nilsso, R.H.1    Ryberg, M.2    Sjökvist, E.3    Abarenkov, K.4
  • 8
    • 1942423770 scopus 로고    scopus 로고
    • Prokaryote diversity and taxonomy: Current status and future challenges
    • Oren A. Prokaryote diversity and taxonomy: current status and future challenges. Phil Trans R Soc Lond B. 2004;359:623-38.
    • (2004) Phil Trans R Soc Lond B , vol.359 , pp. 623-638
    • Oren, A.1
  • 9
    • 35748954014 scopus 로고    scopus 로고
    • Prokaryotic taxonomy and phylogeny in the genomic era: Advancements and challenges ahead
    • Konstantinidis K, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol. 2007;10:504-9.
    • (2007) Curr Opin Microbiol , vol.10 , pp. 504-509
    • Konstantinidis, K.1    Tiedje, J.M.2
  • 10
    • 77955330350 scopus 로고    scopus 로고
    • Microbiological Common Language (MCL): A standard for electronic information exchange in the Microbial Commons
    • Verslyppe B, Kottman R, de Smet W, de Baets B, de Vos P, Dawyndt P. Microbiological Common Language (MCL): a standard for electronic information exchange in the Microbial Commons. Res Microbiol. 2010; 161:439-45.
    • (2010) Res Microbiol , vol.161 , pp. 439-445
    • Verslyppe, B.1    Kottman, R.2    de Smet, W.3    de Baets, B.4    de Vos, P.5    Dawyndt, P.6
  • 11
    • 0032449087 scopus 로고    scopus 로고
    • Ecology versus taxonomy: Is there a middle ground?
    • 387-388
    • Nielsen DL, Shiel RJ, Smith FJ. Ecology versus taxonomy: is there a middle ground? Hydrobiologia. 1998;387-388:451-7.
    • (1998) Hydrobiologia , pp. 451-457
    • Nielsen, D.L.1    Shiel, R.J.2    Smith, F.J.3
  • 12
    • 66249131497 scopus 로고    scopus 로고
    • Global sequencing: A review of current molecular data and new methods available to assess microbial diversity
    • Christen R. Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microb Environ. 2008;23:253-68.
    • (2008) Microb Environ , vol.23 , pp. 253-268
    • Christen, R.1
  • 13
    • 57649143377 scopus 로고    scopus 로고
    • An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity
    • Ryberg M, Kristiansson E, Sjökvist E, Nilsson RH. An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity. New Phytol. 2009;181:471-7.
    • (2009) New Phytol , vol.181 , pp. 471-477
    • Ryberg, M.1    Kristiansson, E.2    Sjökvist, E.3    Nilsson, R.H.4
  • 14
    • 79959660525 scopus 로고    scopus 로고
    • A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software means for their detection and reorientation
    • Nilsson RH, Veldre V, Wang Z, et al. A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software means for their detection and reorientation. Mycoscience. 2010 (in press).
    • (2010) Mycoscience
    • Nilsson, R.H.1    Veldre, V.2    Wang, Z.3
  • 15
    • 41149158774 scopus 로고    scopus 로고
    • Proposal to 'Wikify' GenBank meets stiff resistance
    • Pennisi E. Proposal to 'Wikify' GenBank meets stiff resistance. Science. 2008;319:1598-9.
    • (2008) Science , vol.319 , pp. 1598-1599
    • Pennisi, E.1
  • 16
    • 12244283680 scopus 로고    scopus 로고
    • Modeling the percolation of annotation errors in a database of protein sequences
    • Gilks WR, Audit B, de Angelis D, Tsoka S, Ouzounis CA. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics. 2002;18:1641-9.
    • (2002) Bioinformatics , vol.18 , pp. 1641-1649
    • Gilks, W.R.1    Audit, B.2    de Angelis, D.3    Tsoka, S.4    Ouzounis, C.A.5
  • 17
    • 84881114409 scopus 로고    scopus 로고
    • ADD 2 CO_AUTHORS.Preserving accuracy in GenBank
    • Bidartondo MI. ADD 2 CO_AUTHORS. Preserving accuracy in GenBank. Science. 2008;319:1616.
    • (2008) Science , vol.319 , pp. 1616
    • Bidartondo, M.I.1
  • 18
    • 77956292257 scopus 로고    scopus 로고
    • An open source chimera checker for the fungal ITS region
    • Nilsson RH, Abarenkov K, Veldre V, et al. An open source chimera checker for the fungal ITS region. Mol Ecol Res. 2010;10:1076-81.
    • (2010) Mol Ecol Res , vol.10 , pp. 1076-1081
    • Nilsson, R.H.1    Abarenkov, K.2    Veldre, V.3
  • 19
    • 77954748234 scopus 로고    scopus 로고
    • The UNITE database for molecular identification of fungi-recent updates and future perspectives
    • Abarenkov K, Nilsson RH, Larsson K-H, et al. The UNITE database for molecular identification of fungi-recent updates and future perspectives. New Phytol. 2010;186:281-5.
    • (2010) New Phytol , vol.186 , pp. 281-285
    • Abarenkov, K.1    Nilsson, R.H.2    Larsson, K.-H.3
  • 20
    • 77952765171 scopus 로고    scopus 로고
    • Current state and perspectives of fungal DNA barcoding and rapid identification procedures
    • Begerow D, Nilsson RH, Unterseher M, Maier W. Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol. 2010;87:99-108.
    • (2010) Appl Microbiol Biotechnol , vol.87 , pp. 99-108
    • Begerow, D.1    Nilsson, R.H.2    Unterseher, M.3    Maier, W.4
  • 21
    • 77954172720 scopus 로고    scopus 로고
    • A constructive step towards selecting a DNA barcode for fungi
    • Eberhardt U. A constructive step towards selecting a DNA barcode for fungi. New Phytol. 2010;187:265-8.
    • (2010) New Phytol , vol.187 , pp. 265-268
    • Eberhardt, U.1
  • 22
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse E, Quast C, Knittel K, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res. 2007;35:7188-96.
    • (2007) Nucl Acids Res , vol.35 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3
  • 23
    • 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. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. App Environ Microbiol. 2006;72:5069-72.
    • (2006) App Environ Microbiol , vol.72 , pp. 5069-5072
    • Desantis, T.Z.1    Hugenholtz, P.2    Larsen, N.3
  • 24
    • 19344366809 scopus 로고    scopus 로고
    • UNITE: A database providing web-based methods for the molecular identification of ectomycorrhizal fungi
    • Kõljalg U, Larsson K-H, Abarenkov K, et al. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005;166:1063-8.
    • (2005) New Phytol , vol.166 , pp. 1063-1068
    • Kõljalg, U.1    Larsson, K.-H.2    Abarenkov, K.3
  • 25
    • 56849106496 scopus 로고    scopus 로고
    • The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    • Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008;6:e280.
    • (2008) PLoS Biol , vol.e280 , pp. 6
    • Dethlefsen, L.1    Huse, S.2    Sogin, M.L.3    Relman, D.A.4
  • 26
    • 70349482733 scopus 로고    scopus 로고
    • 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
    • Bueé M, Reich M, Murat C, et al. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol. 2009;184:449-56.
    • (2009) New Phytol , vol.184 , pp. 449-456
    • Bueé, M.1    Reich, M.2    Murat, C.3
  • 27
    • 77956292194 scopus 로고    scopus 로고
    • The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)
    • Öpik M, Vanatoa A, Vanatoa E, et al. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol. 2010;188:223-41.
    • (2010) New Phytol , vol.188 , pp. 223-241
    • Öpik, M.1    Vanatoa, A.2    Vanatoa, E.3
  • 28
    • 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. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537-41.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 7537-7541
    • Schloss, P.D.1    Westcott, S.L.2    Ryabin, T.3
  • 29
    • 5044240973 scopus 로고    scopus 로고
    • Bellerophon; a program to detect chimeric sequences in multiple sequence alignments
    • Huber T, Faulkner G, Hugenholtz P. Bellerophon; a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics. 2004;20:2317-9.
    • (2004) Bioinformatics , vol.20 , pp. 2317-2319
    • Huber, T.1    Faulkner, G.2    Hugenholtz, P.3
  • 31
    • 26444480932 scopus 로고    scopus 로고
    • Taxonomer: A relational data model for managing information relevant to taxonomic research
    • Pyle RL. Taxonomer: a relational data model for managing information relevant to taxonomic research. Phyloinformatics. 2003;1:1-54.
    • (2003) Phyloinformatics , vol.1 , pp. 1-54
    • Pyle, R.L.1
  • 32
    • 34250341823 scopus 로고    scopus 로고
    • A higher-level phylogenetic classification of the Fungi
    • Hibbett DS, Binder M, Bischoff JF, et al. A higher-level phylogenetic classification of the Fungi. Mycol Res. 2007;111:509-47.
    • (2007) Mycol Res , vol.111 , pp. 509-547
    • Hibbett, D.S.1    Binder, M.2    Bischoff, J.F.3
  • 33
    • 33749450254 scopus 로고    scopus 로고
    • A new system for Nematoda: Combining morphological characters with molecular trees, and translating clades into ranks and taxa
    • De Ley P, Blaxter M. A new system for Nematoda: combining morphological characters with molecular trees, and translating clades into ranks and taxa. Nemat Monogr Persp. 2004;2:633-53.
    • (2004) Nemat Monogr Persp , vol.2 , pp. 633-653
    • de Ley, P.1    Blaxter, M.2
  • 34
    • 33745855530 scopus 로고    scopus 로고
    • A modern approach to rotiferan phylogeny: Combining morphological and molecular data
    • Sørensen MV, Giribet G. A modern approach to rotiferan phylogeny: combining morphological and molecular data. Mol Phyl Evol. 2006;40:585-608.
    • (2006) Mol Phyl Evol , vol.40 , pp. 585-608
    • Sørensen, M.V.1    Giribet, G.2
  • 35
    • 70350218974 scopus 로고    scopus 로고
    • An update of the Angiosperm Phylogeny Group classifi{ligature}cation for the orders and families of fl{ligature}owering plants: APG III
    • Angiosperm Phylogeny Group III
    • Angiosperm Phylogeny Group III. An update of the Angiosperm Phylogeny Group classifi{ligature}cation for the orders and families of fl{ligature}owering plants: APG III. Bot J Linn Soc. 2009;161:105-21.
    • (2009) Bot J Linn Soc , vol.161 , pp. 105-121
  • 36
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376-80.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3
  • 38
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure J, Ji H. Next-generation DNA sequencing. Nature Biotechnol. 2008;26:1135-45.
    • (2008) Nature Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 39
    • 69549112742 scopus 로고    scopus 로고
    • Accurate determination of microbial diversity from 454 pyrosequencing data
    • Quince C, Lanzen A, Curtis TP, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Meth. 2009;6:639-41.
    • (2009) Nature Meth , vol.6 , pp. 639-641
    • Quince, C.1    Lanzen, A.2    Curtis, T.P.3
  • 40
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse SM, Welch DM, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol. 2010;12:1889-98.
    • (2010) Environ Microbiol , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 41
    • 77956304094 scopus 로고    scopus 로고
    • Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
    • Reeder J, Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nature Meth. 2010;7:668-9.
    • (2010) Nature Meth , vol.7 , pp. 668-669
    • Reeder, J.1    Knight, R.2
  • 43
    • 72849151143 scopus 로고    scopus 로고
    • Ectomycorrhizal lifestyle in fungi: Global diversity, distribution, and evolution of phylogenetic lineages
    • Tedersoo L, May TW, Smith ME. Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages. Mycorrhiza. 2010;20:217-63.
    • (2010) Mycorrhiza , vol.20 , pp. 217-263
    • Tedersoo, L.1    May, T.W.2    Smith, M.E.3
  • 44
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI BLAST: A new generation in protein database search programs
    • Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI BLAST: a new generation in protein database search programs. Nucl Acids Res. 1997;25:3389-402.
    • (1997) Nucl Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3
  • 45
    • 25644460009 scopus 로고    scopus 로고
    • Approaching the taxonomic affiliation of unidentified sequences in public databases -an example from the mycorrhizal fungi
    • Nilsson RH, Kristiansson E, Ryberg M, Larsson K-H. Approaching the taxonomic affiliation of unidentified sequences in public databases -an example from the mycorrhizal fungi. BMC Bioinform. 2005;6:178.
    • (2005) BMC Bioinform , vol.6 , pp. 178
    • Nilsson, R.H.1    Kristiansson, E.2    Ryberg, M.3    Larsson, K.-H.4
  • 46
    • 77956292565 scopus 로고    scopus 로고
    • An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology
    • Nilsson RH, Veldre V, Hartmann M, et al. An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fung Ecol. 2010;3:284-7.
    • (2010) Fung Ecol , vol.3 , pp. 284-287
    • Nilsson, R.H.1    Veldre, V.2    Hartmann, M.3
  • 47
    • 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. V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. J Microbiol Meth. 2010;83:250-3.
    • (2010) J Microbiol Meth , vol.83 , pp. 250-253
    • Hartmann, M.1    Howes, C.G.2    Abarenkov, K.3    Mohn, W.W.4    Nilsson, R.H.5
  • 48
    • 45749142504 scopus 로고    scopus 로고
    • Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification
    • Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson K-H. Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinf. 2008;4:193-201.
    • (2008) Evol Bioinf , vol.4 , pp. 193-201
    • Nilsson, R.H.1    Kristiansson, E.2    Ryberg, M.3    Hallenberg, N.4    Larsson, K.-H.5
  • 49
    • 77956283658 scopus 로고    scopus 로고
    • 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
    • Tedersoo L, Nilsson RH, Abarenkov K, et al. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol. 2010;188:291-301.
    • (2010) New Phytol , vol.188 , pp. 291-301
    • Tedersoo, L.1    Nilsson, R.H.2    Abarenkov, K.3
  • 50
    • 77952243141 scopus 로고    scopus 로고
    • QIIME allows analysis of high-throughput community sequence data
    • Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequence data. Nature Methods. 2010;7:335-6.
    • (2010) Nature Methods , vol.7 , pp. 335-336
    • Caporaso, J.G.1    Kuczynski, J.2    Stombaugh, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.