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The journal of microbiology v.50 no.2, 2012년, pp.181 - 185   SCIE SCOPUS 피인용횟수: 6
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TBC: A Clustering Algorithm Based on Prokaryotic Taxonomy

Lee, Jae-Hak    (Interdisciplinary Graduate Program in Bioinformatics, Seoul National University   ); Yi, Ha-Na    (Inst. of Molecular Biology and Genetics, Seoul National University   ); Jeon, Yoon-Seong    (Interdisciplinary Graduate Program in Bioinformatics, Seoul National University   ); Won, Sung-Ho    (Department of Statistics, Chung-Ang University   ); Chun, Jong-Sik    (Interdisciplinary Graduate Program in Bioinformatics, Seoul National University  );
  • 초록

    High-throughput DNA sequencing technologies have revolutionized the study of microbial ecology. Massive sequencing of PCR amplicons of the 16S rRNA gene has been widely used to understand the microbial community structure of a variety of environmental samples. The resulting sequencing reads are clustered into operational taxonomic units that are then used to calculate various statistical indices that represent the degree of species diversity in a given sample. Several algorithms have been developed to perform this task, but they tend to produce different outcomes. Herein, we propose a novel sequence clustering algorithm, namely Taxonomy-Based Clustering (TBC). This algorithm incorporates the basic concept of prokaryotic taxonomy in which only comparisons to the type strain are made and used to form species while omitting full-scale multiple sequence alignment. The clustering quality of the proposed method was compared with those of MOTHUR, BLASTClust, ESPRIT-Tree, CD-HIT, and UCLUST. A comprehensive comparison using three different experimental datasets produced by pyrosequencing demonstrated that the clustering obtained using TBC is comparable to those obtained using MOTHUR and ESPRIT-Tree and is computationally efficient. The program was written in JAVA and is available from http://sw.ezbiocloud.net/tbc.

  • 주제어

    TBC .   clustering algorithm .   OTU .   CD-HIT .   UCLUST .   MOTHUR .   ESPRIT-Tree .   BLASTClust .   pyrosequencing .   metagenome.  

  • 참고문헌 (26)

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  • 이 논문을 인용한 문헌 (6)

    1. 2012. "" The journal of microbiology, 50(6): 1081~1085     
    2. Moon, Jong-Geun ; Jung, Man-Young ; Kim, Jong-Geol ; Park, Soo-Je ; Kim, Dae-Shin ; Kim, Jong-Shik ; Rhee, Sung-Keun 2013. "A Unique Prokaryotic Assemblage of Wall Biofilm of a Volcanic Cave (Daesubee) in Jeju" Korean journal of microbiology = 미생물학회지, 49(2): 184~190     
    3. Noh, Eun Soo ; Kim, Young-Sam ; Kim, Dong-Hyun ; Kim, Kyoung-Ho 2013. "Bacterial Diversity in the Guts of Sea Cucumbers (Apostichopus japonicus) and Shrimps (Litopenaeus vannamei) Investigated with Tag-Encoded 454 Pyrosequencing of 16S rRNA Genes" Korean journal of microbiology = 미생물학회지, 49(3): 237~244     
    4. Park, Seung-Hyeon ; Choe, Hyeon-Su ; Gwon, Seon-Yeong ; Yun, Seong-Ro 2014. "" 정보과학회지 = Communications of the Korean Institute of Information Scientists and Engineers, 32(3): 46~53     
    5. 2015. "" Journal of the Korean Society for Applied Biological Chemistry, 58(6): 795~805   
    6. 2016. "" Journal of microbiology and biotechnology, 26(7): 1303~1310     

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