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.
| Original language | English |
|---|---|
| Pages (from-to) | 144-152 |
| Number of pages | 9 |
| Journal | Journal of Microbiological Methods |
| Volume | 65 |
| Issue number | 1 |
| DOIs | |
| State | Published - Apr 2006 |
Funding
This research was supported by the United States Department of Energy, Office of Science, Office of Biological and Environmental Research, Natural and Accelerated Bioremediation Research (NABIR) Program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under contract DE-AC05-00OR22725.
Keywords
- Clone
- Environmental
- Error analysis
- SSU rRNA genes
- Sequencing