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Real Time PCR & Microarray Primer/Probe Design for Cross Species and Taxa Specific Applications
For cross species assays, AlleleID® identifies the conserved regions to design a universal probe. This functionality is especially useful to detect a species or a taxa when designing a diagnostic assay. This functionality is also useful to help study gene expression when genome draft of the organism under study is not available.
When it is not possible to identify a significant conserved region for a set of sequences, AlleleID® attempts to design a "Mismatch Tolerant" probe. The probe may include up to the specified number of mismatched bases which are located as close as possible to the 5' end.
Also included is the "Minimal Set" option that helps you design minimum number of probe sets that uniquely identify a sequence reducing the overall assay cost.
Design qPCR and Microarray Assays for Related Organisms
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® MGB, TaqMan® probes, Molecular Beacons and real time PCR primers. AlleleID® also offers support for designing microarray experiments for detecting alternative splicing events.
AlleleID® Provides a Number of Options for Species Identification
Unique Probes with Unique Primers: When the probe type chosen is Unique, AlleleID® designs probes to identify each sequence in the Bind To box, one probe per sequence. The program searches for base positions that are unique to each individual sequence in the alignment. The probes are centered as close as possible over these unique bases, so that even when the mismatch is only one base, the assay succeeds.
Real Time PCR Primer and Probe Design with AlleleID® & Beacon Designer™
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