Comprehensive web-based platform for advanced PCR design, genotyping, synthetic biology, molecular diagnostics, and sequence analysis
Kalendar R.
9 December 2025Cell Press
Molecular Therapy Nucleic Acids
2025#36Issue 4
We present a comprehensive web-based platform that integrates a suite of molecular biology tools tailored for PCR-based applications. Key features include custom multiplex tiling PCR panel design for amplicon sequencing, loop-mediated isothermal amplification (LAMP), allele-specific PCR genotyping assay development, Gibson assembly, oligonucleotide analysis and design, and the de novo identification, classification, and visualization of repetitive sequences. The platform supports a wide range of PCR primer design tasks, including standard, multiplex, reverse, long-range, quantitative fluorescence (TaqMan and MGB probe), and bisulfite PCR. In silico PCR analysis ensures primer and probe specificity across diverse applications such as gene discovery via homology analysis, molecular diagnostics, DNA profiling, and repeat sequence identification. The multiplex tiling PCR tool is optimized for both next-generation and third-generation sequencing technologies. LAMP primer design includes support for loop primers that target eight distinct regions of the DNA template. The allele-specific PCR module enables genotyping of single nucleotide polymorphisms, insertions/deletions, multi-nucleotide variants, and haplotypes at specific loci. Additionally, the platform facilitates genome-wide identification, masking, and clustering of repetitive elements, including interspersed repeats and low-complexity sequences such as simple sequence repeats and telomeres. All tools are freely accessible at https://primerdigital.com/tools/.
Gibson assembly , in silico PCR , KASP , Kompetitive allele-specific PCR genotyping , LAMP , loop-mediated isothermal amplification , MT: bioinformatics , PCR primer and probe design , primer analysis , repeat identification
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Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Biocentre 3, P.O. Box 65, Viikinkaari 1, Helsinki, 00014, Finland
National Laboratory Astana, Nazarbayev University, 53 Kabanbay batyr Ave., Astana, 010000, Kazakhstan
Helsinki Institute of Life Science (HiLIFE)
National Laboratory Astana
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