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References apply to all FasPCR update, if you use FastPCR in your work please cite:
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
References
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- 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.
- Rachwal PA, Fox KR 2007. Quadruplex melting. Methods, 43:291-301.
- Xu Z, Wang H 2007. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Research, 35:W265-8.
- Burge S, Parkinson GN, Hazel P, Todd AK, Neidle K 2006. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Research, 34:5402-5415.
- Watkins NE, SantaLucia JJ 2005. Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Research, 33(19):6258-6267.
- Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and Genome Research, 110:462-467.
- 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.
- Orlov YL, Potapov VN 2004. Complexity: an internet resource for analysis of DNA sequence complexity. Nucleic Acids Research, 32:W628-W633.
- Rho M, Choi JH, Kim S, Lynch M, Tang H 2004. De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics, 8:90.
- SantaLucia JJ, Hicks D 2004. The thermodynamics of DNA structural motifs. Annual Review of Biophysics and Biomolecular Structure, 33:415-40.
- Lefebvre A, Lecroq T, Dauchel H, Alexandre J 2003. FORRepeats: detects repeats on entire chromosomes and between genomes. Bioinformatics, 19(3):319-26.
- McCarthy EM, McDonald JF 2003. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics, 19(3):362-367.
- Nazarenko I, Lowe B, Darfler M, Ikonomi P, Schuster D, Rashtchian A 2002. Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore. Nucleic Acids Research, 30:e37
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Manual
- Download
- FastPCR Java application
- Online tools for PCR, qPCR, LAMP, analyzing primers, setting up reactions, and calculations
- The program structure
- Import sequence(s)
- Toolbar
- Primers analysis and compatibility
- PCR primers design generalities
- PCR primers and probes design command lines
- Melting temperature calculation
- Calculation of optimal annealing temperature
- Prepare for PCR analysis
- Quick PCR commands help
- Examples
- Output Result
- The secondary (non-specific) binding test (alternative amplification) for primer or probe
- Multiplex primer design
- In silico PCR or primers (probes) searching
- Group-specific (family-specific primer set) and unique PCR primers design
- Probes design
- PCR amplification protocol
- Bioinformatics tools
- Database
- Alignment
- The restriction endonuclease analysis
- References
- Citations
- End user license agreement
- Purchase FastPCR licenses
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