Presets Reference

Pre-configured parameter sets for common PCR applications

PrimerLab includes optimized presets for common PCR applications. Presets provide pre-configured parameters that you can use as-is or customize.

Viewing Presets

# List all available presets
primerlab preset list

# Show details of a specific preset
primerlab preset show long_range

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Available Presets

Standard Presets

Preset	Amplicon Size	Tm Range	QC Mode	Best For
standard_pcr	100-1000 bp	57-63°C	standard	General research
diagnostic_pcr	80-200 bp	58-62°C	strict	Clinical testing
long_range	3000-10000 bp	62-68°C	strict	Large gene fragments
cloning_pcr	200-3000 bp	58-68°C	standard	Molecular cloning
sequencing_pcr	300-800 bp	58-62°C	standard	Sanger sequencing
dna_barcoding	400-700 bp	50-60°C	relaxed	Species identification
rt_pcr	80-150 bp	58-62°C	strict	Reverse transcription

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Preset Details

diagnostic_pcr

High-specificity primers for clinical/diagnostic applications.

Use Cases: Pathogen detection, genetic testing, point-of-care

Parameter	Value
Primer Size	20-28 bp (opt: 22)
Tm	58-62°C (opt: 60°C)
GC%	45-55%
Product Size	80-200 bp
QC Mode	strict

preset: diagnostic_pcr

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long_range

Optimized for amplifying long DNA fragments (3-10+ kb).

Use Cases: Full-length gene amplification, large deletions, genomic regions

Parameter	Value
Primer Size	25-35 bp (opt: 28)
Tm	62-68°C (opt: 65°C)
GC%	40-60%
Product Size	3000-10000 bp
QC Mode	strict

Note: Requires specialized polymerases (e.g., LA Taq, LongAmp).

preset: long_range

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cloning_pcr

Primers designed for molecular cloning with restriction sites.

Use Cases: Gene cloning, subcloning, expression vector construction, Gibson assembly

Parameter	Value
Primer Size	25-40 bp (opt: 30)
Tm	58-68°C (opt: 62°C)
GC%	40-60%
Product Size	200-3000 bp
QC Mode	standard

preset: cloning_pcr

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dna_barcoding

DNA barcoding applications (COI, rbcL, ITS, etc.).

Use Cases: Species identification, biodiversity surveys, phylogenetics

Parameter	Value
Primer Size	20-28 bp (opt: 23)
Tm	50-60°C (opt: 55°C)
GC%	35-70%
Product Size	400-700 bp
QC Mode	relaxed

Note: Relaxed mode allows for diverse templates across taxa.

preset: dna_barcoding

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rt_pcr

Reverse transcription PCR for cDNA amplification.

Use Cases: Gene expression analysis, mRNA detection

Parameter	Value
Primer Size	18-25 bp
Tm	58-62°C
Product Size	80-150 bp
QC Mode	strict

preset: rt_pcr

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Using Presets

In Configuration File

preset: diagnostic_pcr

input:
  sequence_path: ./my_gene.fasta

# Override specific parameters if needed
parameters:
  tm:
    opt: 62.0  # Override default 60°C

Via CLI

# Use preset directly
primerlab run pcr --preset diagnostic_pcr --sequence gene.fasta

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Customizing Presets

Presets provide defaults, but you can override any parameter:

preset: long_range

# Your overrides take precedence
parameters:
  product_size_range: [[5000, 15000]]  # Extend range
  tm:
    opt: 68.0  # Higher Tm for very long amplicons

qc:
  mode: relaxed  # Override strict to relaxed

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See Also

• Configuration Reference
• Customization Guide
• CLI Reference