PerlPrimer Owen Marshall

PerlPrimer is a free, open-source graphical user interface (GUI) application designed to simplify and automate primer design for standard PCR, bisulfite PCR, real-time PCR (QPCR), and sequencing. It provides researchers in molecular biology and genetics with a powerful tool to streamline their workflow.

Key Features:

• Primer-Dimer Calculation: Efficiently calculates potential primer-dimers to minimize unwanted amplification.
• Sequence Retrieval: Automatically retrieves genomic or cDNA sequences from Ensembl, including both sequences for QPCR.
• BLAST Search Integration: Enables BLAST searches using the NCBI server or a local server to validate primer specificity.
• Export Compatibility: Results can be saved or exported in tab-delimited format for compatibility with spreadsheet applications.
• ORF and CpG Detection: Includes algorithms for detecting open reading frames (ORFs) and CpG islands.
• Cloning Sequence Addition: Automatically adds cloning sequences, ensuring they are in-frame with the target sequence.
• QPCR Automation: Simplifies QPCR primer design by eliminating the need for manual intron-exon boundary entry.

Audience & Benefit:

Ideal for researchers in molecular biology and genetics who require precise and efficient primer design. PerlPrimer enhances workflow efficiency, reduces errors, and provides highly accurate predictions of primer melting temperatures using J. SantaLucia's nearest-neighbour thermodynamic parameters and the von Ahsen salt correction formula. This ensures optimal amplification yield under specified PCR conditions.

Technical Details:

Written in Perl and Perl/Tk, PerlPrimer is cross-platform compatible and has been tested on Microsoft Windows, GNU/Linux, and macOS. It integrates with Spidey (NCBI) for QPCR functionality and uses REBASE data for cloning site annotations. The program can be installed via winget.

Note: While the software is widely used in successful experiments, no guarantee is made regarding primer reliability.