PrimerPy is a GUI utility for QPCR primer design.

New release of PrimerPy (Tortilla) 0.97a, available via Downloads page.

major feature upgrade, plus separate module for primer quality check

The Windows installer (tested for winXP only) should have everything one needs. While PrimerPy should be platform independent. See below for installing from source code.

For other platforms or playing with source code, you will need:

1. Python 2.4+, (download from http://www.python.org ; should already shipped with most Linux distributions)
2. wxPython 2.7+, (download from http://www.wxpython.org ; Linux users can use the version in distro repository)
3. Primer3 (http://primer3.sourceforge.net, use binary or compile it yourself - very straight forward installation.)
4. then download the PrimerPy source code from our Downloads page, unpack to your preferred directory
5. run primerpy.py, you should be promoted to configure Primer3 path and places you want to store your data. Save your configuration and restart PrimerPy. That's it.

Development model

As open source, our release is not fully baked, bullet-proof software, though it should be stable and usable, and the primer design quality should take on any commercial software. Users are a vital part of open source development. We improve upon reports and suggestions from users. The importance of an open source QPCR primer design program is not that it's free, but an open science where it is possible for people to study the mechanisms under the hood, to build and improve on them.

How PrimerPy designs primers

PrimerPy enforces a very stringent policy in selecting primers. It is critical to avoid self complementarity among primers, especially 3'-end complementarity. Even properties of Tm, GC percentage and size for primers are also considered. The current version sometimes sacrifices amplicon length for primer quality. If no primers meet the criteria, primers of less quality may be given with a warning.

We have had high success rate with this design strategy. But this program is still a work of progress. Please verify your results carefully. Also a general word: make sure you have the best template sequence to start with. Try to use the 3' end if that's where your reverse transcription starts. To blast your primer on EST database is a way to check specificity.

Please use the Google group http://groups.google.com/group/primerpy to report bugs and give feedback. Thanks!

PrimerPy was previously hosted at: http://www.bioinformatics.org/primerpy/. Our thanks to Bioinformatics.org.