PerlPrimer 1.1.21.

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