SPADA Docs
Multiplex primer dimer check
Check for all possible primer dimer interactions Compute cross-hybridizations of all primer candidates against all amplicons in silico analysis and combinations of singleplexes Capture singleplex performance metrics Tools that allow for replacement of poor performing primers Tools that allow for replacement of poor performing primers in silico analysis and combinations of singleplexes Tools for analyzing existing assays using new target variants Software summary of primer/probe performance Analyze input and performance metrics to determine best practices
input for multiplex algorithm
Multiplex primer-amplicon check
Compute cross-hybridizations of all primer candidates against all amplicons Multiplex algorithm needs to minimize false amplicons to allow even amplification of all targets Determine optimum combination of singplexes that are mutually compatible with eachother Capture singleplex performance, link to input file information, Allow for future A.I. meta-analysis Hold constant primers that work, redesign primers for targets that don't work Hold constant primers that work, redesign primers for targets that don't work Determine optimum combination of singplexes that are mutually compatible with eachother
Multiplex primer-background check Compute false amplicons of all primers against background database
Multiplexing
Experimental validation Re-design
Determine performance of singleplexes Redesign of failed singleplexes
Redesign of failed mutliplexes
Multiplexing
Experimental validation
Determine performance of multiplex
Capture multiplexplex performance metrics Capture multiplex performance, link to input file information, Allow for future A.I. meta-analysis
Post-design analysis
Assay stewardship
Ensure that existing assays work on new target variants
Final report
Summary of final design: thermodynamic, heuristic scores, specificity, sequence alignment validate and verify predefined standards for traceability, accuracy, reliability, and precision
Metrology
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