Species Specificity Check

Feature documentation: Species Specificity Check

Analyze primer specificity across multiple species to detect cross-reactivity.

Overview

The species specificity module helps ensure your primers target only the intended species and don’t cross-react with related organisms.

Key Features:

• Multi-species FASTA loading
• Primer binding site detection across species
• Cross-reactivity scoring (0-100 scale)
• Specificity matrix visualization
• Off-target species warnings

CLI Usage

Basic Usage

primerlab species-check \
  --primers primers.json \
  --target target_species.fasta \
  --output ./species_output

With Off-target Species

primerlab species-check \
  --primers primers.json \
  --target human.fasta \
  --offtargets mouse.fasta,rat.fasta,chimp.fasta \
  --output ./species_output

Excel Report

primerlab species-check \
  --primers primers.json \
  --target target.fasta \
  --offtargets offtarget1.fasta,offtarget2.fasta \
  --format excel \
  --output ./species_output

API Usage

from primerlab.api.public import check_species_specificity_api

# Define primers
primers = [
    {"name": "Gene1", "forward": "ATGC...", "reverse": "GCTA..."},
    {"name": "Gene2", "forward": "TACG...", "reverse": "CGTA..."},
]

# Define templates
target_seq = "ATGCGATC..." # Target species sequence
offtarget_seqs = {
    "Mouse": "ATGCGGTC...",
    "Rat": "ATGCGCTC...",
}

# Run check
result = check_species_specificity_api(
    primers=primers,
    target_template=target_seq,
    target_name="Human",
    offtarget_templates=offtarget_seqs
)

print(f"Score: {result['overall_score']}/100 ({result['grade']})")
print(f"Specific: {result['is_specific']}")

Configuration

Default config: config/species_check_default.yaml

species_check:
  min_match_percent: 70.0   # Min match % to consider binding
  max_mismatches: 5         # Max mismatches allowed
  offtarget_threshold: 80.0 # % binding to flag as problematic

Output Files

File	Description
species_analysis.json	Full analysis data
species_report.md	Human-readable report
species_analysis.xlsx	Excel with matrix

Scoring

Grade	Score	Interpretation
A	90-100	Excellent - highly specific
B	80-89	Good - minor off-target
C	70-79	Acceptable - some cross-reactivity
D	60-69	Poor - significant cross-reactivity
F	0-59	Fail - major cross-reactivity

Warnings

The module generates warnings for:

• Primers with >80% binding to off-target species
• Primers with weak binding to target species
• Multiple off-target binding sites