| Title | A Method for Comparing Multiple Bacterial Community Structures from 16S rDNA Clone Library Sequences |
|---|---|
| Author | Inae Hur1 and Jongsik Chun 1 , 2 * |
| Address | 1 Interdisciplinary Program in Bioinformatics; 2 School of Biological Sciences,Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea |
| Bibliography | Journal of Microbiology, 42(1),9-13, 2004, |
| DOI | |
| Key Words | bioinformatics, microbial community, 16S rRNA, JAVA, hierarchical clustering |
| Abstract | Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/. |
| Download PDF | 421-080.pdf |