SPADA Draft Documents

Below, the weaknesses are described for each of the steps of the traditional approaches and 209 alternative modern methods are recommended that are database-driven, utilize physical 210 chemistry modeling, and utilize modern design algorithms and computational resources.

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Figure 5. Traditional Primer design approach.

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Modern Primer Design Paradigm

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Modern sequence databases

Perhaps the most important new contribution to the field of PCR is the availability of modern 218 sequence databases – they are a treasure trove that can be used to improve the design of the PCR 219 assay to maximize coverage (i.e. the number of variants that are efficiently amplified by a given 220 PCR reaction) and also guide the testing of a PCR assay by identifying potential false positives 221

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