TaqMan® Probes: AlleleID® designs optimal TaqMan® probes free of dimers, repeats and runs to ensure signal fidelity.
TaqMan® MGB Probes: AlleleID® supports the design of TaqMan® MGB probes which are typically shorter as compared to the regular TaqMan® probes.
Multiplex & Allele Identification Assays: AlleleID® supports multiplexing for up to four sequences, avoids cross homologies with all dual labeled probes and primers preventing competition in multiplex reactions. Designs wild and mutant TaqMan® probes for SNP identification.
Evaluate Pre-designed TaqMan® Probes Based Assays: Pre-designed primer sets can be evaluated and a compatible TaqMan® probe designed. Similarly, a pre-designed TaqMan® probe can be evaluated and compatible primers designed. You can even import the primers designed in the SYBR® Green primer design mode and then design a compatible probe.
Graphical View: Displays a graphical view of TaqMan® probe secondary structures.
Read about how TaqMan® probes work.
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.
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.