PRIMEval

PRIMEval predicts and screens hybridization and interaction events in multiplex oligonucleotide assays to optimize assay design and identify potential by-products that reduce amplification efficiency.

Key Features:

• Integration of algorithms: Integrates three distinct algorithms with differing specificity levels to enable tailored in silico evaluation of multiplex assays.
• In silico hybridization prediction: Predicts oligonucleotide hybridization events including formation of resulting products and probes, self-dimers, cross-dimers, and hairpins.
• Artifact screening: Identifies primer dimer formation, unspecific hybridization events, unspecific by-products, and primer depletion that can reduce amplification efficiency.
• Data input: Performs evaluations using user-derived datasets and whole-genome sequencing (WGS) data.
• Thermodynamic analysis: Applies thermodynamic predictions to elucidate the origins of observed artifacts in multiplex assays.
• Assay formats: Targets multiplex polymerase chain reaction (PCR) and microarray assay design and evaluation.

Scientific Applications:

• Multiplex PCR optimization: Supports design and refinement of multiplex PCR assays by predicting interfering interactions and by-products.
• Microarray assay development: Aids microarray probe design and screening for cross-hybridization and secondary-structure artifacts.
• High-throughput genomic studies: Enables screening of complex oligonucleotide panels against whole-genome sequencing (WGS) datasets to anticipate assay behavior.
• Molecular diagnostics: Helps reduce assay artifacts that compromise amplification efficiency and diagnostic accuracy.

Methodology:

Integrates three distinct algorithms to perform in silico evaluations on user-derived datasets, predicting hybridization events, self-dimers, cross-dimers and hairpins, and combines whole-genome sequencing (WGS) data with thermodynamic predictions to elucidate the origins of observed artifacts.