| Title |
TBC: A Clustering Algorithm Based on Prokaryotic Taxonomy |
| Author |
Jae-Hak Lee1, Hana Yi2, Yoon-Seong Jeon1,3, Sungho Won4, and Jongsik Chun1,2,5* |
| Address |
1Interdisciplinary Graduate Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea, 2Inst. of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Republic of Korea, 3Chunlab, Inc., Bldg 138 Rm 318, Seoul National University, Seoul 151-742, Republic of Korea, 4Department of Statistics, Chung-Ang University, Seoul 156-756, Republic of Korea, 5School of Biological Sciences and Advanced Inst. of Convergence Tech., Seoul National University, Seoul 151-742, Republic of Korea |
| Bibliography |
Journal of Microbiology, 50(2),181-185, 2012,
|
| DOI |
|
| Key Words |
TBC, clustering algorithm, OTU, CD-HIT, UCLUST, MOTHUR, ESPRIT-Tree, BLASTClust, pyrosequencing, metagenome |
| Abstract |
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, ESPRITTree,
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. |
