메뉴 건너뛰기




Volumn 2014, Issue 1, 2014, Pages

Swarm: Robust and fast clustering method for amplicon-based studies

Author keywords

Barcoding; Environmental diversity; Molecular operational taxonomic units

Indexed keywords

RNA 16S;

EID: 84907710189     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.593     Document Type: Article
Times cited : (660)

References (26)
  • 5
    • 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(19):2460-2461 DOI 10.1093/bioinformatics/btq461.
    • (2010) Bioinformatics , vol.26 , Issue.19 , pp. 2460-2461
    • Edgar, R.C.1
  • 6
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: accelerated for clustering the next-generation sequencing data
    • Fu L, Niu B, Zhu Z, Wu S, Li W. 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28(23):3150-3152 DOI 10.1093/bioinformatics/bts565.
    • (2012) Bioinformatics , vol.28 , Issue.23 , pp. 3150-3152
    • Fu, L.1    Niu, B.2    Zhu, Z.3    Wu, S.4    Li, W.5
  • 7
    • 79959655657 scopus 로고    scopus 로고
    • DNACLUST: accurate and efficient clustering of phylogenetic marker genes
    • Ghodsi M, Liu B, Pop M. 2011. DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC Bioinformatics 12(1):271 DOI 10.1186/1471-2105-12-271.
    • (2011) BMC Bioinformatics , vol.12 , Issue.1 , pp. 271
    • Ghodsi, M.1    Liu, B.2    Pop, M.3
  • 8
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh O. 1982. An improved algorithm for matching biological sequences. Journal of Molecular Biology 162(3):705-708 DOI 10.1016/0022-2836(82)90398-9.
    • (1982) Journal of Molecular Biology , vol.162 , Issue.3 , pp. 705-708
    • Gotoh, O.1
  • 10
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse SM, MarkWelch D, Morrison HG, Sogin ML. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology 12(7):1889-1898 DOI 10.1111/j.1462-2920.2010.02193.x.
    • (2010) Environmental Microbiology , vol.12 , Issue.7 , pp. 1889-1898
    • Huse, S.M.1    MarkWelch, D.2    Morrison, H.G.3    Sogin, M.L.4
  • 12
    • 84878548639 scopus 로고    scopus 로고
    • Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units
    • Koeppel AF, Wu M. 2013. Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units. Nucleic Acids Research 41(10):5175-5188 DOI 10.1093/nar/gkt241.
    • (2013) Nucleic Acids Research , vol.41 , Issue.10 , pp. 5175-5188
    • Koeppel, A.F.1    Wu, M.2
  • 15
    • 79954584273 scopus 로고    scopus 로고
    • Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences
    • Nebel M, Pfabel C, Stock A, Dunthorn M, Stoeck T. 2011. Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences. Environmental Microbiology Reports 3(2):154-158 DOI 10.1111/j.1758-2229.2010.00200.x.
    • (2011) Environmental Microbiology Reports , vol.3 , Issue.2 , pp. 154-158
    • Nebel, M.1    Pfabel, C.2    Stock, A.3    Dunthorn, M.4    Stoeck, T.5
  • 16
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48(3):443-453 DOI 10.1016/0022-2836(70)90057-4.
    • (1970) Journal of Molecular Biology , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 17
    • 84950632109 scopus 로고
    • Objective criteria for the evaluation of clustering methods
    • Rand WM. 1971. Objective criteria for the evaluation of clustering methods. Journal of the American Statistical Association 66(336):846-850 DOI 10.1080/01621459.1971.10482356.
    • (1971) Journal of the American Statistical Association , vol.66 , Issue.336 , pp. 846-850
    • Rand, W.M.1
  • 18
    • 84863304598 scopus 로고    scopus 로고
    • Vienna: R Foundation for Statistical Computing
    • R Development Core Team. 2014. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing. Available at http://www. R-project.org.
    • (2014) R: a language and environment for statistical computing
  • 19
    • 79957630864 scopus 로고    scopus 로고
    • Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
    • Rognes T. 2011. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinformatics 12(1):221 DOI 10.1186/1471-2105-12-221.
    • (2011) BMC Bioinformatics , vol.12 , Issue.1 , pp. 221
    • Rognes, T.1
  • 21
    • 0000821965 scopus 로고
    • On the theory and computation of evolutionary distances
    • Sellers PH. 1974. On the theory and computation of evolutionary distances. SIAM Journal on Applied Mathematics 26:787-793 DOI 10.1137/0126070.
    • (1974) SIAM Journal on Applied Mathematics , vol.26 , pp. 787-793
    • Sellers, P.H.1
  • 22
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS. 1981. Identification of common molecular subsequences. Journal of Molecular Biology 147(1):195-197 DOI 10.1016/0022-2836(81)90087-5.
    • (1981) Journal of Molecular Biology , vol.147 , Issue.1 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 24
    • 0028028182 scopus 로고
    • Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
    • Stackebrandt E, Goebel BM. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 44(4):846-849 DOI 10.1099/00207713-44-4-846.
    • (1994) International Journal of Systematic Bacteriology , vol.44 , Issue.4 , pp. 846-849
    • Stackebrandt, E.1    Goebel, B.M.2
  • 25
    • 0027113212 scopus 로고
    • Approximate string-matching with q-grams and maximal matches
    • Ukkonen E. 1992. Approximate string-matching with q-grams and maximal matches. Theoretical Computer Science 92(1):191-211 DOI 10.1016/0304-3975(92)90143-4.
    • (1992) Theoretical Computer Science , vol.92 , Issue.1 , pp. 191-211
    • Ukkonen, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.