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Real Time PCR Primer Design

AlleleID® designs real time PCR primers that are optimized for the following chemistries viz. TaqMan®, TaqMan® MGB, molecular beacons and FRET. These real time PCR primers are specific, efficient and compatible with the probe that they work with:

  • Primer Specificity: Primers are designed by avoiding significant cross homologies identified by automatically interpreting BLAST search results.

  • Primer Efficiency: Primer efficiency is enhanced by automatically avoiding template structures identified by folding the template.

  • Multiplex PCR Primer Design: Design support for multiplex assays is included. Up to four sequences in the TaqMan® design mode and five sequences in the molecular beacon design mode can be multiplexed.

  • Use Pre-designed Primers: Include a well proven primer set for a template and design a compatible probe.

AlleleID® can also be used to design SYBR® Green real time PCR primers. There is a separate SYBR® Green real time primer design mode in AlleleID®.

Species Identification Assays/Cross Species Assays/Allele Identification Assays

AlleleID® aligns sequences using ClustalW and analyzes conserved and species specific regions. You can then use the program for real time PCR primer design (SYBR® Green primer design included) and dual labeled probe design (TaqMan® probes, TaqMan® MGB probes and molecular beacons). These assays are designed to detect only the strain (strain detection) or species of interest from the mix.

Sophisticated Algorithms for Assay Success

Highly specific oligos are designed by avoiding regions of significant homologies found by automatically interpreting BLAST search results. Real time PCR primer & probe efficiency is enhanced by avoiding template secondary structures. "Minimal Set", one of the most innovative features in the program, helps design the fewest number of allele specific oligonucleotide primers and dual labeled probes that uniquely identify each of the desired species/strain/taxa from the mix, lowering assay costs. For taxa or cross species assays, this feature is especially useful when the group or taxa is highly dissimilar. For a partial set of pre-designed, proven set of primers, AlleleID® can design compatible primers and probes for the rest of sequences for species identification or taxa specific assays.


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