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Beacon Designer™


  • Generate Report: You can create an attractively formatted report for the assays you designed. It should be helpful in record keeping and for sharing information with colleagues. The report helps visualize the positions of the primers and probes on the sequence, includes a list of the alternate primers and probes, displays primers, probe, amplicon and sequence properties and the design parameters used.

  • Sequence Details View: Comprehensive information of all sequences in a project is available locally using the built-in database and the sequence details can be viewed using your browser from within the program.

  • Sequence Visualization: The primers and probes designed are displayed graphically in the Sequence View pane along with the regions of cross-homology and potential template structures.

  • Input Formats: Supports sequences in standard GenBank and FASTA format. Using the multiple retrieval facility, sequences can be loaded from local drives.

  • SNP Loading: Easily loads thousands of SNPs from the variation descriptors in standard GenBank variation files.

  • View Output in Spreadsheet: Results can be viewed and manipulated in any spreadsheet like MS Excel, Lotus 123 or OpenOffice spreadsheet.

  • Export Sequence View: Export the "sequence view" along with the oligos design results in text or HTML format.

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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