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AlleleID is a comprehensive desktop tool designed to address the challenges of pathogen detection, bacterial identification or taxa/species discrimination using microarrays and TaqMan and molecular beacon qPCR assays. With ClustalW multiple sequence alignment at its core, AlleleID can design species specific/cross species probes for microarrays or TaqMan/molecular beacon qPCR assays. You could use both the techniques; verify microarray results using qPCR, or perhaps, make microarrays based on probes through qPCR.
This application is not free. Pricing is provided by quote, which can be generated here.