Supplementary materials for the article "Joint selection of primers and restriction enzymes based on distinguishability of three diploid genotypes"

Data, scripts and results for the article "Joint selection of primers and restriction enzymes based on distinguishability of three diploid genotypes" (submitted to Mathematical Biology and Bioinformatics). All calculations used RFLP Picker 1.1.0 (https://github.com/adrobi/rflppicker/releases/tag/v1.1.0, commit 42ad9e5fd7c79609f36666e72ac16c1b1d1faf81). The archive contains: (1) a computational experiment on 80 synthetic sequences with 1, 5, 10 and 20 Primer3 primer pairs per variant, including the data generator, inputs, full result tables, sensitivity analysis and timing; (2) a retrospective validation on 17 published, experimentally validated PCR-RFLP assays in sheep and rice from PubMed Central, with the pre-registered selection protocol and a dated log of deviations, curated assay data, scripts and per-assay results; (3) a comparison with SNP2CAPS, CAPS Designer, indCAPS and dCAPS Finder 2.0 on the same variants, including raw responses of the web services. Supplementary_Materials.docx (also as PDF, in Russian) describes the archive, the methods and all results, and explains how to reproduce the calculations. No biological samples were collected; only published information was used. Full texts of the screened articles and the SNP2CAPS program are not redistributed; the scripts retrieve the articles again, and a patch for SNP2CAPS is provided.