Primer & Probe Design Solutions

PrimerDigital provides assay design and bioinformatics services for PCR, qPCR, multiplex panels, and sequence-based marker development—supported by repeat-aware filtering and in-silico specificity analysis.

You receive

Ordering-ready primer/probe tables
Specificity/off-target assessment
Multiplex interaction screening
Implementation notes (cycling, pooling)

Assay design

General PCR primer design

Standard, long-range, inverted, and sequencing-oriented PCR designs.

Multiplex PCR panels

Multiplex and high-plex primer sets with pool partitioning and interaction-aware filtering.

qPCR and probe assays

TaqMan-style probes, MGB probes, molecular beacons, LUX primers, and related chemistries.

SSR and repeat-associated markers

SSR locus primers and repeat-based polymorphism assays for plants and animals.

Primer/probe redesign

Improve performance of existing assays: efficiency, specificity, and platform constraints.

Group-specific amplification

Primers that amplify related sequences while enabling discrimination of polymorphisms.

Project services

Gene walking (identify unknown genomic sequence adjacent to known region)
Multiplex PCR primer development projects
Polymorphism detection for multi-locus/homologous gene sets
Repeat-based polymorphism (SSR, retrotransposons, tandem repeats)

In silico experiment planning and assay feasibility checks
Probe design projects for priority targets
Targeted amplicon sequencing panel design (Illumina/ONT)
Documentation and deliverables for lab execution

Software development

Custom algorithms for primer/probe design and filtering
Automation of assay workflows and reporting
Tools tailored to customer pipelines and databases
Containerized or web-based delivery (where appropriate)

DNA & RNA extraction services

Extraction from diverse sources and tissue amounts
Process options for challenging sample matrices
QC checkpoints aligned to downstream needs
Cost-effective outsourcing for routine workflows

If you need a strict chemistry constraint (e.g., no phenol/chloroform), mention it and we will propose an approach.

How to request a design

Send targets (FASTA or coordinates), organism/build, assay type (PCR/qPCR/multiplex), desired amplicon length range, and constraints (chemistry, SNP position, panel size).

Discuss your project

We can propose a design strategy and deliverables aligned to your platform and workflow.