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Cross Species Detection
Changes in the DNA makeup of the organisms such as single nucleotide polymorphisms, during the course of evolution, have led to the diversity in phenotypic traits. Generations after generations, inherit these changes and contribute towards the biodiversity of species. Despite all these changes, there are still stretches of DNA which remain conserved during evolution. Such conserved regions or sequences are useful in suggesting phylogenetically similar groups, identification of an organism within a group or understanding the extent of its biodiversity amongst the flora of a particular area.
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.
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.
Taxa Specific/Cross Species identification: Probes with Mismatched Bases and Optimal Primers
Minimal Probes with Optimal Primers: When the homology among the aligned sequences is very low and both the designs mentioned above (a single taxa specific probe set or probe set with mismatch tolerance) are not feasible, AlleleID® designs the minimum number of probes possible to detect all the sequences in an alignment. The program designs probes for the majority consensus first and then for the minority consensus and remaining individual sequences. This design is very useful, especially for studying phylogenetic relationships among sequences obtained from different geographical locations.
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