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Beacon Designer™

Design HRMA Primers

Beacon Designer™ offers a comprehensive solution for Mutation detection and SNP genotyping using High Resolution Melting Analysis (HRMA), a more cost-effective method than probe-based genotyping analysis. The program employs proprietary algorithms that enable designing the best High Resolution Melting Analysis primers for detecting all types of mutations including DIPs, MNPs, SNPs classes I and II for heterozygotes and homozygotes.

The primers are designed flanking the mutation of interest to generate the shortest possible amplicons with detectable melting temperature variation, taking into consideration all the parameters essential for High Resolution Melting Analysis. The primers are designed avoiding template secondary structures, assuring efficient primer extension. The designed primers can be BLAST searched against nucleotide databases, including the redundant nr database at NCBI, to verify their specificity.

You can use pre-designed or published or well proven forward or reverse primers and have Beacon Designer™ evaluate them for you. For example, for a given forward primer, Beacon Designer™ can design a reverse primer for HRMA assays.

Automate Your Real Time PCR Primer and Probe Design

Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.

Specific and Efficient Design: How Beacon Designer™ Makes it Possible?

You can BLAST search sequences and search for template structures from within the program. The results of both these searches are used while designing primers and probes. The regions that exhibit significant cross homologies and template structures are avoided automatically during the design.


  • SYBR® Green Primer Design
  • TaqMan® Probe Design
  • Multiplex Real Time PCR Assay Design
  • HRMA Primer Design
  • MethyLight TaqMan® Design
  • Molecular Beacon Design
  • NASBA® Assay Design
  • FRET Probe Design
  • Scorpions® Design
  • Avoiding Cross Homology- For Specific Oligo Design
  • Avoid Template Structures- Increase Primer Efficiency
  • Oligo Rating


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