title: Confidence intervals of similarity values determined for cloned SSU rRNA genes from environmental samples.
abstract: The goal of this research was to investigate the influence of the error rate of sequence determination on the differentiation of cloned SSU rRNA gene sequences for assessment of community structure. SSU rRNA cloned sequences from groundwater samples that represent different bacterial divisions were sequenced multiple times with the same sequencing primer. From comparison of sequence alignments with unedited data, confidence intervals were obtained from both a 'double binomial' model of sequence comparison and by non-parametric methods. The results indicated that similarity values below 0.9946 are likely derived from dissimilar sequences at a confidence level of 0.95, and not sequencing errors. The results confirmed that screening by direct sequence determination could be reliably used to differentiate at the species level. However, given sequencing errors comparable to those seen in this study, sequences with similarities above 0.9946 should be treated as the same sequence if a 95% confidence is desired.
authors.affiliation: Department of Microbiology, Miami University, Oxford, Ohio 45056, USA.
authors.forename: M W
authors.initials: MW
authors.lastname: Fields
authors.forename: J C
authors.initials: JC
authors.lastname: Schryver
authors.forename: C C
authors.initials: CC
authors.lastname: Brandt
authors.forename: T
authors.initials: T
authors.lastname: Yan
authors.forename: J Z
authors.initials: JZ
authors.lastname: Zhou
authors.forename: A V
authors.initials: AV
authors.lastname: Palumbo
mesh_terms: D001483:Base Sequence; D016001:Confidence Intervals; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D005618:Fresh Water; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D014871:Water Microbiology
chemical_list: D004269:DNA, Bacterial; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S