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AlleleID® is a comprehensive desktop tool designed to address the challenges of bacterial identification, pathogen detection or species identification. With ClustalW multiple sequence alignment at its core, AlleleID® can be used to design species identification/cross species probes for microarrays or real time PCR, including SYBR® Green, TaqMan® probes, TaqMan® MGB probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events.
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.
Location of the primers and probes is defined by the target sequence for real time PCR primer design. Real time PCR assays can also be designed to detect alternative splicing events. The program uses an algorithm to analyze the alignment. AlleleID® design utilizes target specific information for the lowest possible price. This minimizes false positive primers and probes. The program also generates an optimized multiple sequence alignment to identify conserved region between the target and reference (seed sequence). AlleleID® uses only sequences of interest in the multiple sequence alignment to the amplified region. 7211a4ac4a