Package: SNPAssayR 1.0.1

SNPAssayR: SNP Genotyping Assay Design and Visualization

Designs cleaved amplified polymorphic sequence (CAPS), derived CAPS (dCAPS), conventional amplification refractory mutation system (ARMS) and tetra-primer ARMS assays for single-locus, biallelic single nucleotide polymorphisms. Evaluates sequence-compatible primer binding, reconstructs ideal polymerase chain reaction products and computes theoretical complete restriction digestion and conditional genotype profiles. Transparent preference ranking, scientific visualizations and reproducible exports retain assumptions, missing specificity evidence and bounded search limitations. An optional offline 'shiny' interface uses the independently available analysis functions. Predictions do not establish experimental amplification, digestion efficiency or genome-wide specificity. Implements perfect-match nearest-neighbor thermodynamics from SantaLucia (1998) <doi:10.1073/pnas.95.4.1460>, single-substitution site-creation dCAPS based on Neff et al. (1998) <doi:10.1046/j.1365-313X.1998.00124.x>, and conditional ARMS designs based on Newton et al. (1989) <doi:10.1093/nar/17.7.2503> and Ye et al. (2001) <doi:10.1093/nar/29.17.e88>.

Authors:Prashant Yadav [aut, cre], Vinod Kumar [aut], Vijay Veer Singh [aut], ICAR-Indian Institute of Rapeseed-Mustard Research [cph]