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