PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulfite 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