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bio-primer-design-qpcr-primers

Maintainer FreedomIntelligence · Last updated April 1, 2026

Design qPCR/RT-PCR primers with efficiency and specificity optimization.

OpenClawNanoClawAnalysisReproductionbio-primer-design-qpcr-primers🧠 bioos extended suitebioos extended bioinformatics suitedesign

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-primer-design-qpcr-primers

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Design primers and internal probes for quantitative PCR using primer3-py.
global_args = { 'PRIMER_PICK_INTERNAL_OLIGO': 1, 'PRIMER_PRODUCT_SIZE_RANGE': [[70, 150]], # Probe Tm should be 8-10C higher than primers 'PRIMER_OPT_TM': 60.0, 'PRIMER_INTERNAL_OPT_TM': 70.0, # Probe should be closer to forward primer 'PRIMER_INTERNAL_MIN_SIZE': 18, 'PRIMER_INTERNAL_MAX_SIZE': 30, # Avoid long poly-X runs in probe 'PRIMER_INTERNAL_MAX_POLY_X': 3, }.

Source Doc

Excerpt From SKILL.md

For SYBR Green, design primers without probe

result = primer3.design_primers( seq_args={'SEQUENCE_TEMPLATE': sequence}, global_args={ 'PRIMER_PICK_LEFT_PRIMER': 1, 'PRIMER_PICK_RIGHT_PRIMER': 1, 'PRIMER_PICK_INTERNAL_OLIGO': 0, # No probe 'PRIMER_PRODUCT_SIZE_RANGE': [[70, 200]], # Short for qPCR 'PRIMER_OPT_TM': 60.0, 'PRIMER_MIN_TM': 58.0, 'PRIMER_MAX_TM': 62.0, 'PRIMER_MAX_SELF_ANY': 4, # Strict for SYBR specificity 'PRIMER_MAX_SELF_END': 2, 'PRIMER_PAIR_MAX_COMPL_ANY': 4, 'PRIMER_PAIR_MAX_COMPL_END': 2, } )


## Mark the exon junction position

exon_junction = 150  # Position where exons meet

result = primer3.design_primers(
    seq_args={
        'SEQUENCE_TEMPLATE': sequence,
        'SEQUENCE_OVERLAP_JUNCTION_LIST': [exon_junction],  # Primer must span
    },
    global_args={
        'PRIMER_PRODUCT_SIZE_RANGE': [[70, 150]],
        'PRIMER_OPT_TM': 60.0,
        'PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION': 4,  # Min bases on each side
    }
)

Design primers for multiple targets with compatible Tms

targets = [ {'name': 'gene1', 'seq': sequence1, 'target': [100, 30]}, {'name': 'gene2', 'seq': sequence2, 'target': [150, 30]}, ]

results = [] for target in targets: result = primer3.design_primers( seq_args={ 'SEQUENCE_TEMPLATE': target['seq'], 'SEQUENCE_ID': target['name'], 'SEQUENCE_TARGET': target['target'], }, global_args={ 'PRIMER_PICK_INTERNAL_OLIGO': 1, 'PRIMER_PRODUCT_SIZE_RANGE': [[70, 150]], 'PRIMER_OPT_TM': 60.0, # Same Tm for all 'PRIMER_MAX_TM': 61.0, 'PRIMER_MIN_TM': 59.0, 'PRIMER_INTERNAL_OPT_TM': 70.0, } ) results.append(result)

Use cases

Use bio-primer-design-qpcr-primers for genomics and bioinformatics workflows.
Apply bio-primer-design-qpcr-primers to sequencing, variant, or omics analysis tasks.