Example 1

In this example, we want to see how well a particular universal primer set for the 16S rRNA gene is at describing a phylogenetic grouping of interest.  The primer set we shall consider is that described by Muyzer et al[1]. Used mainly in denaturing gradient gel electrophoresis (DGGE) studies, this primer set is designed to amplify a ~200 bp region of the 16S rRNA gene target from all bacterial genomes.  How well does this primer set describe the CFB bacterial division (recently re-named the Bacteroidetes phylum; called the Flexibacter-Cytophaga-Bacteroides group in the RDP release 8.1 used here), as defined by the RDP database?  In addition, how well does the primer set target some additional CFB bacteria, not currently included within the RDP?

We will action the following steps:
  1. Construct database.
  2. Enter primer set.
  3. Do analysis.
  4. View results.
Next Page.

[1] Muyzer, G., de Waal, E. C., & Uitterlinden, A. G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology. 59(3). 695-700.