Primer Prospector

Primer Prospector is a pipeline of programs to design and analyze PCR primers.

De novo primers can be generated from a set of aligned fasta sequences and these primers, or known primers from literature, can be scored against target sequences. Predicted primer performance can be visualized in summary graphs showing overall primer performance or across specific taxonomies.

Primer Prospector is built in Python using the open-source PyCogent toolkit.

Download Primer Prospector

  • Stable Release: The current release is 1.0.1, which you can download here.

  • Development Version: Primer Prospector is under development. To get the latest development version of Primer Prospector, you access our Sourceforge repository. While this code is subject to minor changes in interface, it will provide access to the latest and greatest features. The official web documentation is likely to be out-of-date with respect to the development software. You should instead refer to the svn documentation in pprospector/doc. Check out the latest version of Primer Prospector using svn with the command:

    svn co pprospector

Installing and using Primer Prospector

New users should begin with the Primer Prospector installation guide. After installing Primer Prospector, you should move on to the Primer Prospector overview tutorial to generate and analyze several primers. For general information about Primer Prospector, you’ll want to refer to the Primer Prospector documentation

Contact Us

The primary contact for Primer Prospector is William Walters (use @ for AT and . for DOT: williamDOTaDOTwaltersATcoloradoDOTedu).

Users can submit bug reports and feature requests via Sourceforge

Citing Primer Prospector

If you use Primer Prospector for any published research, please include the following citation:

  • PrimerProspector: de novo design and taxonomic analysis of PCR primers. William A. Walters (1,6), J. Gregory Caporaso (2,6), Christian L. Lauber (3), Donna Berg-Lyons (3), Noah Fierer (4), and Rob Knight (2,5). Bioinformatics (2011) 27(8): 1159-1161 first published online February 23, 2011 doi:10.1093/bioinformatics/btr087
  1. Department of Molecular, Cellular, and Developmental Biology. University of Colorado at Boulder, Boulder, CO, USA.
  2. Department of Chemistry and Biochemistry. University of Colorado at Boulder, Boulder, CO, USA.
  3. Cooperative Institute for Research in Environmental Sciences. University of Colorado at Boulder, Boulder, CO, USA.
  4. Department of Ecology and Evolutionary Biology. University of Colorado at Boulder, Boulder, CO, USA.
  5. Howard Hughes Medial Institute, Boulder, CO, USA.
  6. These authors contributed equally to this work.