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title: "Configuration Reference" description: "YAML configuration file reference for PrimerLab"

Complete reference for all PrimerLab configuration parameters.

Configuration File Structure

input:
  sequence: "ATCGATCG..."  # or sequence_path
  sequence_path: /path/to/sequence.fasta

parameters:
  tm:
    min: 57.0
    opt: 60.0
    max: 63.0
  
  primer_size:
    min: 18
    opt: 20
    max: 25
  
  product_size:
    min: 100
    max: 300
  
  gc:
    min: 40.0
    max: 60.0

output:
  format: json  # json, csv, text
  directory: ./output

Parameter Reference

Input Parameters

Parameter Type Description
sequence string Raw DNA sequence
sequence_path path Path to FASTA file

Tm (Melting Temperature)

Parameter Default Range Description
tm.min 57.0 50-70 Minimum Tm
tm.opt 60.0 55-65 Optimal Tm
tm.max 63.0 58-72 Maximum Tm

Primer Size

Parameter Default Range Description
primer_size.min 18 15-25 Minimum length
primer_size.opt 20 18-22 Optimal length
primer_size.max 25 20-30 Maximum length

Product Size

Parameter Default Description
product_size.min 100 Minimum amplicon
product_size.max 300 Maximum amplicon

Recommendations by workflow:

Workflow Min Max Notes
Standard PCR 200 1000 Flexible
qPCR 70 150 Short preferred
Long-range PCR 1000 10000 Specialized enzymes

GC Content

Parameter Default Description
gc.min 40.0 Minimum GC%
gc.max 60.0 Maximum GC%

qPCR-Specific Parameters

parameters:
  probe:
    tm:
      min: 65.0
      opt: 68.0
      max: 72.0
    size:
      min: 20
      max: 30
Parameter Default Description
probe.tm.opt 68.0 Probe Tm (5-10°C > primers)
probe.size.min 20 Minimum probe length
probe.size.max 30 Maximum probe length

Advanced Parameters

Salt Concentrations

parameters:
  salt:
    monovalent: 50.0   # mM (Na+, K+)
    divalent: 1.5      # mM (Mg2+)
    dntp: 0.2          # mM

Thermodynamic Thresholds

parameters:
  thermo:
    hairpin_dg_max: -2.0    # kcal/mol
    homodimer_dg_max: -5.0  # kcal/mol
    heterodimer_dg_max: -5.0

Output Configuration

output:
  format: json       # json, csv, text, html
  directory: ./output
  include_audit: true
  include_rationale: true

Example Configurations

Standard PCR

input:
  sequence_path: ./gene.fasta

parameters:
  tm:
    opt: 60.0
  product_size:
    min: 200
    max: 500

qPCR with TaqMan Probe

input:
  sequence_path: ./target.fasta

parameters:
  tm:
    opt: 60.0
  product_size:
    min: 70
    max: 150
  probe:
    tm:
      opt: 68.0

Long-Range PCR

input:
  sequence_path: ./region.fasta

parameters:
  tm:
    opt: 65.0
  product_size:
    min: 2000
    max: 10000
  primer_size:
    opt: 25

See Also