In-silico PCR API

Python API reference for In-silico PCR API

Virtual PCR simulation and primer binding analysis.

Module

from primerlab.core.insilico import (
    run_insilico_pcr,
    InsilicoPCR,
    analyze_binding,
    calculate_corrected_tm,
    check_three_prime_stability
)

---

run_insilico_pcr()

Run virtual PCR simulation.

Signature

def run_insilico_pcr(
    forward: str,
    reverse: str,
    template_path: Path = None,
    template_seq: str = None,
    max_mismatches: int = 2,
    min_3prime_match: int = 3,
    circular: bool = False
) -> InsilicoPCRResult

Parameters

Parameter	Type	Default	Description
forward	str	required	Forward primer sequence (5’→3’)
reverse	str	required	Reverse primer sequence (5’→3’)
template_path	Path	None	Path to template FASTA
template_seq	str	None	Template sequence string
max_mismatches	int	2	Max mismatches allowed
min_3prime_match	int	3	Min perfect 3’ match
circular	bool	False	Treat template as circular

Returns

InsilicoPCRResult:

• products: List of predicted amplicons
• forward_binding: Binding site analysis
• reverse_binding: Binding site analysis
• is_specific: True if single product

Example: Basic Validation

from primerlab.core.insilico import run_insilico_pcr

result = run_insilico_pcr(
    forward="ATGGTGAGCAAGGGCGAGGAG",
    reverse="TTACTTGTACAGCTCGTCCATGCC",
    template_path="gfp.fasta"
)

print(f"Products found: {len(result.products)}")
if result.is_specific:
    product = result.products[0]
    print(f"Amplicon size: {product.size} bp")
    print(f"Position: {product.start} - {product.end}")

Example: With Template String

template = "ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGG..."

result = run_insilico_pcr(
    forward="ATGGTGAGCAAGGGCGAGGAG",
    reverse="CCCGGTGAACAGCTCCTCGCC",  # reverse complement
    template_seq=template
)

for product in result.products:
    print(f"Size: {product.size} bp, Likelihood: {product.likelihood}%")

---

analyze_binding()

Analyze primer binding at a specific site.

Signature

def analyze_binding(
    primer_seq: str,
    target_seq: str,
    position: int = 0
) -> BindingSite

Returns

BindingSite:

• position: Binding position on template
• mismatches: Number of mismatches
• mismatch_positions: List of mismatch locations
• three_prime_dg: 3’ end stability (ΔG)
• estimated_tm: Corrected Tm based on mismatches
• validation_notes: Warnings if any

Example

from primerlab.core.insilico import analyze_binding

binding = analyze_binding(
    primer_seq="ATGGTGAGCAAGGGCGAGGAG",
    target_seq="ATGGTGAGCAAGGGCGAGGAG"  # Perfect match
)

print(f"Mismatches: {binding.mismatches}")
print(f"3' ΔG: {binding.three_prime_dg:.2f} kcal/mol")
print(f"Estimated Tm: {binding.estimated_tm:.1f}°C")

---

calculate_corrected_tm() (v0.3.4)

Calculate Tm corrected for mismatches.

Signature

def calculate_corrected_tm(
    primer_seq: str,
    target_seq: str,
    base_tm: float,
    mismatches: int,
    correction_per_mismatch: float = 2.5
) -> float

Example

from primerlab.core.insilico import calculate_corrected_tm

# Base Tm 60°C with 2 mismatches
corrected_tm = calculate_corrected_tm(
    primer_seq="ATGGTGAGCAAGGGCGAGGAG",
    target_seq="ATGGTGAGCAAGGGTGAGGAG",  # 1 mismatch
    base_tm=60.0,
    mismatches=1
)
print(f"Corrected Tm: {corrected_tm}°C")  # ~57.5°C

---

check_three_prime_stability() (v0.3.4)

Check 3’ end stability and generate warnings.

Signature

def check_three_prime_stability(
    three_prime_dg: float,
    threshold_strong: float = -9.0,
    threshold_weak: float = -3.0
) -> Optional[str]

Returns

• None if 3’ stability is OK
• Warning string if too stable or too weak

Example

from primerlab.core.insilico import check_three_prime_stability

warning = check_three_prime_stability(three_prime_dg=-10.5)
if warning:
    print(f"Warning: {warning}")
# Output: "Warning: 3' end too stable (ΔG=-10.5), may cause mispriming"

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See Also

• Public API
• Models Reference