Scoring

Scoring System

Understanding how PrimerLab ranks primer candidates from 0 to 100.

The Design Philosophy

PrimerLab uses a penalty-based scoring system. Every primer pair starts with a conceptual score of 0 (perfect) penalty, and accumulates penalties for deviations from optimal parameters.

For user display, these penalties are converted to a 0-100 Quality Score, where 100 is perfect.

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Scoring Factors

The total score is a weighted sum of deviations for the following factors:

1. Tm Deviation (Weight: 25%)

How far is the primer’s Tm from the opt_tm setting?

• Optimality: Perfect match = 0 penalty.
• Penalty: Increases as Tm moves away from optimum.
• Pair Difference: Large difference between Forward and Reverse Tm incurs a heavy penalty.

2. GC Content (Weight: 20%)

How close is the GC% to 50%?

• Optimality: 50% = 0 penalty.
• Range: Deviations outside 40-60% incur increasing penalties.

3. Self-Complementarity (Weight: 20%)

Does the primer bind to itself?

• Metric: Alignment score / Delta G.
• Penalty: High affinity self-binding = high penalty.

4. Pair Complementarity (Weight: 20%)

Do the Forward and Reverse primers bind to each other?

• Metric: Alignment score / Delta G.
• Penalty: This is weighted heavily because primer-dimers ruin experiments.

5. Product Size (Weight: 5%)

is the amplicon length close to opt_product_size?

• Less critical than thermodynamic properties, but useful for optimization.

6. 3’ End Stability (Weight: 10%)

Is the 3’ end stable but not too sticky?

• Penalties for G/C runs at the 3’ tip.

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Quality Grade Scale

Score	Grade	Interpretation
95-100	⭐ Excellent	Almost theoretical perfection. Rare.
90-94	✅ Great	Standard stringent result. Highly reliable.
80-89	👌 Good	Likely to work well. Minor deviations.
70-79	⚠️ Fair	May require optimization (Mg++, Temp).
< 70	❌ Poor	Significant risk of failure. Try to redesign.

Customizing Weights

(Advanced) You can tweak these weights in your configuration if you prioritize one factor over others (e.g., strict Tm over GC%):

scoring:
  weights:
    tm: 0.4
    gc: 0.1
    dimer: 0.3
    compl: 0.2