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Volumn 29, Issue 10, 2013, Pages 1268-1274

Density-based hierarchical clustering of pyro-sequences on a large scale - The case of fungal ITS1

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA;

EID: 84877947899     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt149     Document Type: Article
Times cited : (16)

References (17)
  • 1
    • 77954336858 scopus 로고    scopus 로고
    • ITS as an environmental DNA barcode for fungi: An in silico approach reveals potential PCR biases
    • Bellemain, E. et al. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol., 10, 189.
    • (2010) BMC Microbiol. , vol.10 , pp. 189
    • Bellemain, E.1
  • 2
    • 84869417474 scopus 로고    scopus 로고
    • Comparing clustering and pre-processing in taxonomy analysis
    • Bonder, M.J. et al. (2012) Comparing clustering and pre-processing in taxonomy analysis. Bioinformatics, 28, 2891-2897.
    • (2012) Bioinformatics , vol.28 , pp. 2891-2897
    • Bonder, M.J.1
  • 4
    • 80051732979 scopus 로고    scopus 로고
    • ESPRIT-Tree: Hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
    • Cai, Y. and Sun, Y. (2011) ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acids Res., 39, e95.
    • (2011) Nucleic Acids Res. , vol.39
    • Cai, Y.1    Sun, Y.2
  • 5
    • 84880268534 scopus 로고    scopus 로고
    • Improving the prediction of plant species distribution and community composition by adding edaphic to topo-climatic variables
    • Epub ahead of print, doi: 10.1111/jvs.12002, October 29, 2012
    • Dubuis, A. et al. (2012) Improving the prediction of plant species distribution and community composition by adding edaphic to topo-climatic variables. J. Veg. Sci., [Epub ahead of print, doi: 10.1111/jvs.12002, October 29, 2012].
    • (2012) J. Veg. Sci
    • Dubuis, A.1
  • 6
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R.C. (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
  • 7
    • 79961181125 scopus 로고    scopus 로고
    • UCHIME improves sensitivity and speed of chimera detection
    • Edgar, R.C. et al. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194-2200.
    • (2011) Bioinformatics , vol.27 , pp. 2194-2200
    • Edgar, R.C.1
  • 8
    • 0000008146 scopus 로고
    • Comparing partitions
    • Hubert, L. and Arabie, P. (1985) Comparing partitions. J. Classif., 2, 193-218.
    • (1985) J. Classif. , vol.2 , pp. 193-218
    • Hubert, L.1    Arabie, P.2
  • 9
    • 34948842866 scopus 로고    scopus 로고
    • Accuracy and quality of massively parallel DNA pyrose-quencing
    • Huse, S.M. et al. (2007) Accuracy and quality of massively parallel DNA pyrose-quencing. Genome Biol., 8, R143.
    • (2007) Genome Biol. , vol.8
    • Huse, S.M.1
  • 10
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh, K. and Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol., 30, 772-780.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 11
    • 0028158905 scopus 로고
    • Improving the sensitivity of the sequence profile method
    • Luthy, R., Xenarios, I. and Bucher, P. (1994) Improving the sensitivity of the sequence profile method. Protein Sci., 3, 139-146.
    • (1994) Protein Sci. , vol.3 , pp. 139-146
    • Luthy, R.1    Xenarios, I.2    Bucher, P.3
  • 12
    • 77950645212 scopus 로고    scopus 로고
    • Artificial and natural duplicates in pyrosequencing reads of metagenomic data
    • Niu, B. et al. (2010) Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics, 11, 187.
    • (2010) BMC Bioinformatics , vol.11 , pp. 187
    • Niu, B.1
  • 13
    • 0035292408 scopus 로고    scopus 로고
    • Making sense of score statistics for sequence alignments
    • Pagni, M. and Jongeneel, C.V. (2001) Making sense of score statistics for sequence alignments. Brief. Bioinfo., 2, 51-67.
    • (2001) Brief. Bioinfo. , vol.2 , pp. 51-67
    • Pagni, M.1    Jongeneel, C.V.2
  • 14
    • 69549112742 scopus 로고    scopus 로고
    • Accurate determination of microbial diversity from 454 pyrosequencing data
    • Quince, C. et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods, 6, 639-641.
    • (2009) Nat. Methods , vol.6 , pp. 639-641
    • Quince, C.1
  • 15
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European Molecular Biology Open Software Suite
    • Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 16
    • 0001290045 scopus 로고    scopus 로고
    • PROSITE: A documented database using patterns and profiles as motif descriptors
    • Sigrist, C.J. et al. (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief. Bioinfo., 3, 265-274.
    • (2002) Brief. Bioinfo. , vol.3 , pp. 265-274
    • Sigrist, C.J.1
  • 17
    • 84862928738 scopus 로고    scopus 로고
    • A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis
    • Sun, Y. et al. (2012) A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Brief. Bioinfo., 13, 107-121.
    • (2012) Brief. Bioinfo. , vol.13 , pp. 107-121
    • Sun, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.