Tm Adjustment: Automatically selects a stem of appropriate length for optimal beacon Tm.
Optimal Beacons: Designs beacons free of dimers, repeats, and runs for increased signal strength.
Multiplex Beacons & Primers: Checks molecular beacons for cross homologies with all primers preventing competition in multiplex reactions.
Allele Identification: Designs molecular beacons for detection of both wild and mutant alleles.
Tm Calculation: Highly accurate hairpin Tm calculation.
Evaluate Pre-designed Molecular Beacon Assays: Pre-designed primer sets can be evaluated or primers for a pre-designed molecular probe can be constructed. Similarly, a pre-designed beacon can be evaluated or a beacon can be designed for a pre-designed primer set. This facilitates using SYBR® Green primers for beacon assays which can be used for bacterial identification assays or any other assay.
Lightning Fast: Processes an average cDNA sequence in under a second.
Read about molecular beacons.
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.