primer-design

Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates. Use for designing primer pairs, checking existing primers, exon-junction or isoform-specific assays, variant masking, cloning tails, multiplex compatibility, and interpreting Primer-BLAST results. Includes bounded local in-silico PCR and BLAST screening; distinguishes computational candidates from experimentally validated assays.

Version

1.1

License

MIT

Compatibility

Requires Python 3.11+ and primer3-py 2.3.1 for design and thermodynamics. Local exhaustive screening uses the standard library; BLAST screening additionally needs blastn and makeblastdb on PATH. Network access is needed only for installation, reference retrieval, or external Primer-BLAST.