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

An optional run-time dependency is spidey, for Real Time PCR.

For details and citation:
Marshall OJ. PerlPrimer: cross-platform, graphical primer design for
standard, bisulphite and real-time PCR. Bioinformatics 2004
20(15):2471-2472