메뉴 건너뛰기




Volumn , Issue , 2012, Pages 1023-1034

Efficient clustering of metagenomic sequences using locality sensitive hashing

Author keywords

Local ity sensitive hashing; Metagenomics; Sequence clustering

Indexed keywords

BACTERIA; COMPUTATIONAL EFFICIENCY; DATA MINING;

EID: 84872533735     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1137/1.9781611972825.88     Document Type: Conference Paper
Times cited : (12)

References (27)
  • 3
    • 33745634395 scopus 로고    scopus 로고
    • CD-HIT: A fast pro- gram for clustering and comparing large sets of protein or nucleotide sequences
    • Weizhong Li and Adam Godzik. CD-HIT: A fast pro- gram for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22(13):1658- 1659, 2006.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 4
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than blast
    • Robert C. Edgar. Search and clustering orders of magnitude faster than blast. Bioinformatics, 2010.
    • (2010) Bioinformatics
    • Edgar, R.C.1
  • 5
    • 79952001955 scopus 로고    scopus 로고
    • Clustering 16s rrna for otu prediction: A method of unsupervised bayesian clustering
    • Xiaolin Hao, Rui Jiang, and Ting Chen. Clustering 16s rrna for otu prediction: A method of unsupervised bayesian clustering. Bioinformatics, 27(5):611-618, 2011.
    • (2011) Bioinformatics , vol.27 , Issue.5 , pp. 611-618
    • Hao, X.1    Jiang, R.2    Chen, T.3
  • 6
    • 15444362001 scopus 로고    scopus 로고
    • Introducing dotur, a computer program for de-ning operational taxonomic units and estimating species richness
    • Patrick D. Schloss and Jo Handelsman. Introducing dotur, a computer program for de-ning operational taxonomic units and estimating species richness. Appl. Environ. Microbiol., 71(3):1501-1506, 2005.
    • (2005) Appl. Environ. Microbiol. , vol.71 , Issue.3 , pp. 1501-1506
    • Schloss, P.D.1    Handelsman, J.2
  • 7
    • 72949107142 scopus 로고    scopus 로고
    • Introducing mothur: Open-source, platform-independent, community- supported software for describing and comparing microbial communities
    • D Schloss, Patrick and et. al. Introducing mothur: Open-source, platform-independent, community- supported software for describing and comparing microbial communities. Appl. Environ. Microbiol., 75(23):7537-7541, 2009.
    • (2009) Appl. Environ. Microbiol. , vol.75 , Issue.23 , pp. 7537-7541
    • Schloss, D.1    Patrick2
  • 8
    • 67249096511 scopus 로고    scopus 로고
    • Esprit: Estimating species rich- ness using large collections of 16s rrna pyrosequences
    • Yijun Sun and et. al. Esprit: estimating species rich- ness using large collections of 16s rrna pyrosequences. Nucleic Acids Research, 2009.
    • (2009) Nucleic Acids Research
    • Sun, Y.1
  • 10
    • 77951946180 scopus 로고    scopus 로고
    • Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing
    • Yiqun Cao, Tao Jiang, and Thomas Girke. Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing. Bioinformatics, 26(7):953-959, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 953-959
    • Cao, Y.1    Jiang, T.2    Girke, T.3
  • 12
    • 34248641408 scopus 로고    scopus 로고
    • Fast agglomerative hierarchical clustering algo- rithm using locality-sensitive hashing
    • May
    • Hisashi Koga, Tetsuo Ishibashi, and Toshinori Watan- Abe. Fast agglomerative hierarchical clustering algo- rithm using locality-sensitive hashing. Knowl. Inf. Syst., 12:25-53, May 2007.
    • (2007) Knowl. Inf. Syst. , vol.12 , pp. 25-53
    • Koga, H.1    Ishibashi, T.2    Abe T.W.-3
  • 13
    • 0035024494 scopus 로고    scopus 로고
    • Eficient large-scale sequence com- parison by locality-sensitive hashing
    • Jeremy Buhler. Eficient large-scale sequence com- parison by locality-sensitive hashing. Bioinformatics, 17(5):419-428, 2001.
    • (2001) Bioinformatics , vol.17 , Issue.5 , pp. 419-428
    • Buhler, J.1
  • 14
    • 34948842866 scopus 로고    scopus 로고
    • Accuracy and quality of mas- sively parallel dna pyrosequencing
    • Jul
    • Susan Huse, Julie Huber, Hilary Morrison, Mitchell So- gin, and David Welch. Accuracy and quality of mas- sively parallel dna pyrosequencing. Genome Biology, 8(7):R143+, jul 2007.
    • (2007) Genome Biology , vol.8 , Issue.7
    • Huse, S.1    Huber, J.2    Morrison, H.3    Gin M.S.-4    Welch, D.5
  • 15
    • 66349083859 scopus 로고    scopus 로고
    • Topographical and temporal diversity of the human skin microbiome
    • Elizabeth A. Grice and et. al. Topographical and temporal diversity of the human skin microbiome. Science, 324(5931):1190-1192, 2009.
    • (2009) Science , vol.324 , Issue.5931 , pp. 1190-1192
    • Grice, E.A.1
  • 16
    • 11144354360 scopus 로고    scopus 로고
    • Environmental genome shotgun sequencing of the Sargasso Sea
    • J.C. Venter and et. al. Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304(5667):66, 2004.
    • (2004) Science , vol.304 , Issue.5667 , pp. 66
    • Venter, J.C.1
  • 17
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene cata- logue established by metagenomic sequencing
    • Mar
    • Junjie Qin et al. A human gut microbial gene cata- logue established by metagenomic sequencing. Nature, 464(7285):59-65, Mar 2010.
    • (2010) Nature , vol.464 , Issue.7285 , pp. 59-65
    • Qin, J.1
  • 18
    • 35348968286 scopus 로고    scopus 로고
    • The human microbiome project
    • October
    • Peter J Turnbaugh and et. al. The human microbiome project. Nature, 449(7164):804810, October 2007.
    • (2007) Nature , vol.449 , Issue.7164 , pp. 804810
    • Turnbaugh, P.J.1
  • 19
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denatur- ing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16s rrna
    • G Muyzer, E C de Waal, and A G Uitterlinden. Profiling of complex microbial populations by denatur- ing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16s rrna. Appl. Environ. Microbiol., 59(3):695-700, 1993.
    • (1993) Appl. Environ. Microbiol. , vol.59 , Issue.3 , pp. 695-700
    • Muyzer, G.1    Waal, E.C.D.2    Uitterlinden, A.G.3
  • 20
    • 34147182303 scopus 로고    scopus 로고
    • A detailed analysis of 16s ribosomal rna gene segments for the diagnosis of pathogenic bacteria
    • Soumitesh Chakravorty, Danica Helb, Michele Burday, Nancy Connell, and David Alland. A detailed analysis of 16s ribosomal rna gene segments for the diagnosis of pathogenic bacteria. Journal of Microbiological Methods, 69(2):330- 339, 2007.
    • (2007) Journal of Microbiological Methods , vol.69 , Issue.2 , pp. 330-339
    • Chakravorty, S.1    Helb, D.2    Burday, M.3    Connell, N.4    Alland, D.5
  • 24
    • 28444492998 scopus 로고    scopus 로고
    • Profile-based direct kernels for remote homology detection and fold recognition
    • Dec
    • Huzefa Rangwala and George Karypis. Profile-based direct kernels for remote homology detection and fold recognition. Bioinformatics, 21(23):4239-4247, Dec 2005.
    • (2005) Bioinformatics , vol.21 , Issue.23 , pp. 4239-4247
    • Rangwala, H.1    Karypis, G.2
  • 26
    • 72949091232 scopus 로고    scopus 로고
    • Bacterial community variation in human body habitats across space and time
    • Elizabeth K. Costello and et. al. Bacterial community variation in human body habitats across space and time. Science, 326(5960):1694-1697, 2009.
    • (2009) Science , vol.326 , Issue.5960 , pp. 1694-1697
    • Costello, E.K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.