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Species Identification: Minimal probes with Optimal primers
How Species Were Identified Historically
The field of disease diagnosis and drug development has seen a rapid replacement of culture based methods for bacterial and species identification by faster and more reliable molecular based techniques such as real time PCR and microarrays. The reason for the success for these techniques is the ease with which one can identify a species from a sample collected from complex sources such as air, soil, or water.
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.
Although these double-stranded DNA-binding dyes provide the simplest and cheapest option for real time PCR, the principal drawback to intercalation based detection of PCR product accumulation is that both specific and nonspecific products generate **.
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