title: A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences.
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/.
authors.affiliation: Interdisciplinary Program in Bioinformatics ,Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea.
authors.forename: Inae
authors.initials: I
authors.lastname: Hur
authors.forename: Jongsik
authors.initials: J
authors.lastname: Chun
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics* / Q000254:growth & development*; D016000:Cluster Analysis; D019295:Computational Biology; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000737:chemistry* / Q000302:isolation & purification; D017753:Ecosystem; D004783:Environmental Microbiology; D015723:Gene Library; D020459:Genes, rRNA; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S