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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
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
This requires perl-tk and libwww-perl.
For Real Time PCR, spidey is required.
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