rprimer

rprimer designs degenerate oligonucleotides and PCR assays from multiple DNA sequence alignments as an R/Bioconductor package to enable detection, quantification, sequencing, and genotyping of sequence-variable viruses.

Key Features:

• Degenerate Oligo Design: Creates degenerate primers and probes tailored to regions of high genetic variability to target sequence-variable viruses.
• PCR Assay Development: Supports design of quantitative PCR (qPCR) and reverse transcription-PCR (RT-PCR) assays for detection, quantification, sequencing, and genotyping.
• Input Data: Accepts multiple DNA sequence alignments as the primary input for assay design.
• Outputs: Produces detailed tables (data frames) and dashboard-like plots summarizing oligo candidates and assay designs.
• Primer/Probe Optimization: Selects and reports oligos optimized for variable sequences to improve assay coverage across diverse viral variants.

Scientific Applications:

• Norovirus GI RT-qPCR assay: Used to design an RT-qPCR assay for quantitative detection of norovirus genogroup I (GI) and evaluated on stool samples positive for norovirus GI with amplification and quantification performance comparable to a standardized assay.
• Norovirus GI RT-PCR for sequencing and genotyping: Used to design an RT-PCR assay suitable for Sanger sequencing and polymerase-capsid based genotyping that enabled sequencing and genotyping of all tested norovirus GI samples.

Methodology:

Multiple DNA sequence alignments are input to the package, which processes the alignments to design degenerate oligonucleotides and optimized primers/probes and exports results as data frames and dashboard-like plots.