Confidence intervals for similarity values determined for clonedSSU rRNA genes from environmental samples
The goal of this research was to investigate the influenceof the error rate of sequence determination on the differentiation ofcloned SSU rRNA gene sequences for assessment of community structure. SSUrRNA cloned sequences from groundwater samples that represent differentbacterial divisions were sequenced multiple times with the samesequencing primer. From comparison of sequence alignments with unediteddata, confidence intervals were obtained from both a adouble binomial Tmodel of sequence comparison and by non-parametric methods. The resultsindicated that similarity values below 0.9946 arelikely derived fromdissimilar sequences at a confidence level of 0.95, and not sequencingerrors. The results confirmed that screening by direct sequencedetermination could be reliably used to differentiate at the specieslevel. However, given sequencing errors comparable to those seen in thisstudy, sequences with similarities above 0.9946 should be treated as thesame sequence if a 95 percent confidence is desired.
- Research Organization:
- COLLABORATION - Miami U./Oxford,OH
- DOE Contract Number:
- DE-AC02-05CH11231
- OSTI ID:
- 922709
- Report Number(s):
- LBNL-60420; JMIMDQ; R&D Project: VGTLTH; BnR: KP1102010; TRN: US200803%%448
- Journal Information:
- Journal of Microbiological Methods, Vol. 65, Issue 1; Related Information: Journal Publication Date: April, 2006; ISSN 0167-7012
- Country of Publication:
- United States
- Language:
- English
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