PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.
PerlPrimer's current features include the following:
- Calculation of possible primer-dimers
- Retrieval of genomic or cdna sequences from Ensembl (including both sequences automatically for QPCR)
- Ability to BLAST search primers using the NCBI server or a local server
- Results can be saved or optionally exported in a tab-delimited format that is compatible with most spreadsheet applications.
- ORF and CpG island detection algorithms
- Ability to add cloning sequences to primers, automatically adjusted to be in-frame
- QPCR primer design without manual intron-exon boundary entry
PerlPrimer calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use standard PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified.
PerlPrimer is written in Perl and Perl/Tk. In addition, for QPCR functionality PerlPrimer uses the open-source Spidey executable from NCBI, and restriction enzyme data from the REBASE project is used when adding cloning sites. The program is designed to be cross-platform compatible and has been developed and tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also reported success using the program under Mac OS X.
Please cite the reference below if this program is useful.
Marshall OJ. PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 2004 20(15):2471-2472 [Pubmed]
Publisher’s description
What is PerlPrimer?
PerlPrimer is an open-source program for Windows from Owen Marshall.
Installation and requirements
Official installers exist for 32-bit as EXE (NSIS). The main installer is 3.4 MB. Installation asks for administrator rights. The installer supports unattended (silent) installation.
Popularity and file types
On Windows it registers 1 file type, including .ppr.
Pros / Cons
Pros
- Open source: the code can be inspected and built by anyone
- Documented silent install
- Small download (3.4 MB)
Cons
- No native ARM64 build
- 32-bit only
- Installation needs administrator rights
- No update for more than a year
In short: PerlPrimer is an open-source Windows tool for 32-bit PCs. Updates have slowed down. Administrators can deploy it unattended.
Is PerlPrimer safe to download?
- The file is served by sourceforge.net, the publisher’s own domain
- The download link uses HTTPS
- A SHA256 hash is published, so you can verify the file:
F911658B761F1CA1F09F9A6C11E4540120F7FD7E1A11B328FACD35D03E03E8BB· Open the VirusTotal report for this hash - The link answered when we last checked it (October 22, 2026)
- The source code is public
- ExeAtlas does not host, wrap or modify installers
Related guide: How to check a file’s SHA256 hash on Windows
Recent versions
All 1 versions ›| Version | Date | Size | Files |
|---|---|---|---|
| 1.1.21Latest | November 21, 2011 | 3.4 MB | 32-bit EXE (NSIS) |
Install from the command line
Silent install ›winget install --id OwenMarshall.PerlPrimer -edownload /SRelated guide: How to use winget: install and update apps
Information
- Publisher
- Owen Marshall
- Licence
- GPL-2.0-or-later
- Price
- Free
- Requires
- Windows 11 / 10
- Architecture
- 32-bit
- Installer
- EXE (NSIS)
- Version
- 1.1.21
- Released
- November 21, 2011
- Added to the catalogue
- August 2, 2025
- Versions listed
- 1
- Website
- perlprimer.sourceforge.net
- winget ID
- OwenMarshall.PerlPrimer
File types it opens (1)
Ratings and reviews
No reviews yet. Be the first to rate it.
Frequently asked questions
Is PerlPrimer free?
Yes. PerlPrimer is open-source software under the GPL-2.0-or-later licence.
Is PerlPrimer safe to download?
The download comes from sourceforge.net, which belongs to the publisher; ExeAtlas does not host or change the file. Compare its SHA256 hash with the one shown here, or open the VirusTotal report for that hash.
How do I install PerlPrimer with winget?
Open PowerShell or Windows Terminal and run the winget command shown on this page. winget downloads the official installer and checks its SHA256 hash before running it.
Can PerlPrimer be installed silently?
Yes. The silent install page lists the exact command for each installer.
Does PerlPrimer run on ARM (Windows on Arm)?
There is no ARM64 build; Windows 11 on Arm can run the 32-bit version through emulation.