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Modern Techniques for Cross Species Detection
Real time PCR and microarrays offer a rapid, sensitive, specific and quantitative tool for the diagnosis of pathogens. Diseases are not readily distinguished based on symptoms when there is more than one pathogen in the sample. Microscopic identification requires culturing on specialized media for days to weeks. Recently, real time PCR assays were successfully used in the detection of fungal pathogens such as Rhizoctonia, Pythium, and Fusarium.
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.
Taxa Specific/Cross Species Identification: Conserved Probe with Optimal Primers
Conserved Probe with Optimal Primers: AlleleID® designs a primer pair that would amplify the maximum number of sequences possible in an alignment. There are two choices available for designing primers, Unique and Optimal. For "Unique", the program designs a primer pair to amplify each sequence. Each primer is completely homologous to its template. For "Optimal', the program minimizes the number of primers required to amplify all sequences; taking advantage of the fact that primers can bind to a sequence and amplify it even if they contain a limited number of mismatched bases especially towards the 5' end of the primer.
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.
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