References apply to FastPCR and all Web Tools, if you use it in your work please cite:


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 Download PDF

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 Download PDF

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 Download PDF

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 Download PDF

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 Download PDF

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 Download PDF

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 Download PDF

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 Download PDF

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 Download PDF

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 Download PDF



References

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.