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/.
Keywords
PhylotypeLibraryTemperature gradient gel electrophoresisBiologyclone (Java method)16S ribosomal RNAComputational biologyJavaIdentification (biology)Cluster analysisDNA sequencingFingerprint (computing)GeneticsComputer scienceDNAArtificial intelligenceGeneEcology
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Publication Info
- Year
- 2004
- Type
- article
- Volume
- 42
- Issue
- 1
- Pages
- 9-13
- Citations
- 35
- Access
- Closed
External Links
Citation Metrics
35
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Cite This
Inae Hur,
Jongsik Chun
(2004).
A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences..
PubMed
, 42
(1)
, 9-13.