SPADA Draft Documents

sequence databases for inclusivity, exclusivity, and background. These are used in the k-mer- 455 based target analysis algorithm as well as the thermodynamics-based scanning of oligonucleotide 456 candidates to determine their coverage and specificity. There is also built-in physical chemistry 457 modeling (e.g., dynamic programming algorithms such as MFOLD or OMP ) to compute 458 thermodynamics for unimolecular folding and bimolecular hybridization, and numerical methods 459 for solving the multi-state coupled equilibrium model to determine the amount bound. There is 460 also the critical component for ranking the results using a weighted scoring equation. Lastly, 461 Table 1 provides a summary of essential design criteria that should be included in a modern 462 primer design pipeline. Improving upon these principles will require the recommendations 463 described in the metrology section below. Combining the designs for different singleplex 464 reactions into larger multiplexed format is discussed in the next section. In addition, below we 465 recommend an iterative process of performing experimental validation to develop robust assays.

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468 Figure 7. Modern Consensus Design Paradigm for Pathogen Detection by PCR. 469

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