Contact
For scientific collaboration, licensing, or citation questions: Prof. Ruslan Kalendar.
Recommended citation
Please cite these papers when using FastPCR and PrimerDigital Web Tools.
- Kalendar R 2025. Comprehensive web-based platform for advanced PCR design, genotyping, synthetic biology, molecular diagnostics, and sequence analysis. Molecular Therapy Nucleic Acids, 36(4): 102716. DOI:10.1016/j.omtn.2025.102716

- Kalendar R, Kairov U 2024. Genome-wide tool for sensitive de novo identification and visualisation of interspersed and tandem repeats. Bioinformatics and biology insights, 18: 1-11. DOI:10.1177/11779322241306391

- Kalendar R, Shevtsov A, Otarbay Z, Ismailova A 2024. In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays. Frontiers in Bioinformatics, 4: 1464197. DOI:10.3389/fbinf.2024.1464197

- Kalendar R, Shustov AV, Akhmetollaev IA, Kairov U 2022. Designing allele-specific competitive-extension PCR-based assays for high-throughput genotyping and gene characterization. Frontiers Molecular Biosciences, 9:773956. DOI:10.3389/fmolb.2022.773956

- Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Kurishbayev A, Jatayev S, Hu Y-G, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y 2022. Modified ‘Allele-specific qPCR’ method for SNP genotyping based on FRET. Frontiers in Plant Science, 12:747886. DOI:10.3389/fpls.2021.747886

- Kalendar R 2022. A guide to using FASTPCR software for PCR, in silico PCR, and oligonucleotide analysis. Methods in molecular biology, 2392: 223-243. DOI:10.1007/978-1-0716-1799-1_16

- Kalendar R, Kospanova D, Schulman AH 2021. Transposon-based tagging in silico using FastPCR software. Methods in molecular biology, 2250: 245-256. DOI:10.1007/978-1-0716-1134-0_23

- Kalendar R, Khassenov B, Ramankulov Y, Samuilova O, Ivanov KI 2017. FastPCR: an in silico tool for fast primer and probe design and advanced sequence analysis. Genomics, 109: 312-319. DOI:10.1016/j.ygeno.2017.05.005

- Kalendar R, Tselykh T, Khassenov B, Ramanculov EM 2017. Introduction on using the FastPCR software and the related Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods in Molecular Biology, 1620: 33-64. DOI:10.1007/978-1-4939-7060-5_2

- Kalendar R, Muterko A, Shamekova M, Zhambakin K 2017. In silico PCR tools a fast primer, probe and advanced searching. Methods in Molecular Biology, 1620: 1-31. DOI:10.1007/978-1-4939-7060-5_1

- Kalendar R, Lee D, Schulman AH 2014. FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods in Molecular Biology, 1116: 271-302. DOI:10.1007/978-1-62703-764-8_18

- Kalendar R, Lee D, Schulman AH 2011. Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics, 98(2): 137-144. DOI:10.1016/j.ygeno.2011.04.009

Key references
Thermodynamics and parameterization references used in primer/probe calculations.
- Owczarzy R, Moreira BG, You Y, Behlke MA, Walder JA 2008. Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. Biochemistry, 47(19): 5336-5353.
- Watkins NE, SantaLucia JJ 2005. Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res, 33(19): 6258-6267.
- Owczarzy R, You Y, Moreira BG, Manthey JA, Huang L, Behlke MA, Walder JA 2004. Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures. Biochemistry, 43(12): 3537-3554.
- McTigue, Patricia M, Peterson, Raymond J, and Kahn, Jason D 2004. Sequence-Dependent Thermodynamic Parameters for Locked Nucleic Acid (LNA)-DNA Duplex Formation. Biochemistry, 43:5388-5405.
- SantaLucia J 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS, 95:1460-1465.
- Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH 1998. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37(42):14719-35.