Tutorial

Primrose is a computer program for designing oligonucleotide probes and PCR primers.  Although designed primarily to utilise small subunit ribosomal RNA sequence data, Primrose can be used to design probes and primers for any phylogenetically useful gene.

The following tutorial illustrates how Primrose can be used to identify potentially useful phylogenetic probes using data from the Ribosomal Database Project and other sources. 

For this tutorial, we shall identify a 16S rDNA probe that can target a novel uncultured taxon with the Bacteroidetes phylum.  Ideally, we require a probe that will target exclusively our novel taxon to the exclusion of all other bacteria.

On running the program the we're presented with the following window:



Primrose identifies oligonucleotides by following a four step process:
  1. Construct database.
  2. Specify target taxon.
  3. Find all oligonucleotides which describe this taxon.
  4. Screen these oligonucleotides against the assembled database to find the most suitable oligonucleotide.
Click here to continue.