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Overview

The Assay Design tool uses AI to design PCR primers and probes for your targets. It supports multiplex assay development with dimer screening, fluorophore compatibility, and protocol generation.

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Design Workflow

1

Create a project

Click New Project, enter a name, and select your instrument (Bio-Rad CFX96, ABI 7500, LightCycler 480, etc.).
2

Add targets

For each target, specify:
  • Organism — Target species
  • Gene — Target gene
  • Accession — NCBI accession number
  • Channel — Fluorophore channel (FAM, HEX, VIC, ROX, Cy5, etc.)
3

Generate designs

Click Generate and the AI designs primer/probe sets for each target.
4

Review designs

Each target gets a ranked list of design candidates.
Alex’s screenshot note: Take a screenshot of the design project page showing the target list with organism, gene, and channel columns.

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Design Results

For each target, the AI generates multiple primer/probe candidates ranked by score:

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Visualizations

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Amplicon Map

A D3.js visualization showing primer and probe binding positions on the target gene.

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Radar Chart

Multi-axis chart comparing design candidates across:
  • Tm optimality
  • GC content
  • Amplicon size
  • Penalty score
  • Dimer safety

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Fluorophore Spectra

Emission curves for each channel showing spectral overlap between fluorophores.
Alex’s screenshot note: Take a screenshot of the amplicon map showing primer positions on the gene. Take another of the radar chart comparing 2-3 design candidates.

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Multiplex Check

For multi-target assays, the Multiplex Check screens for:
  • Primer-dimer formation between all primer/probe combinations
  • Compatibility matrix showing safe/problematic pairs
  • DimerZipper visualization for detailed dimer analysis

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Protocol Builder

Generate a ready-to-use PCR protocol:
  • Reaction volume and components
  • Primer/probe concentrations
  • Master mix recipe
  • Cycling conditions (denaturation, annealing, extension)

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Order Sheet

Export your selected designs for ordering:
  • Oligo table with all sequences
  • Copy FASTA — Copy sequences in FASTA format
  • IDT Bulk CSV — Export for IDT ordering
  • Export CSV — General CSV export