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A Guide to Using FASTPCR Software for PCR, In Silico PCR, and Oligonucleotide Analysis

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PCR Primer Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2392))

Abstract

The FastPCR software is an integrated tool environment for PCR primer and probe design and for prediction of oligonucleotide properties. The software provides comprehensive tools for designing primers for most PCR and perspective applications, including standard, multiplex, long-distance, inverse, real-time with TaqMan probe, Xtreme Chain Reaction (XCR), group-specific, overlap extension PCR for multifragment assembling cloning, and isothermal amplification (Loop-mediated Isothermal Amplification). A program is available to design specific oligonucleotide sets for long sequence assembly by ligase chain reaction and to design multiplexed of overlapping and nonoverlapping DNA amplicons that tile across a region(s) of interest for targeted next-generation sequencing, competitive allele-specific PCR (KASP)-based genotyping assay for single-nucleotide polymorphisms and insertions and deletions at specific loci, among other features. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. FastPCR includes various bioinformatics tools for analysis and searching of sequences, restriction I–II–III-type enzyme endonuclease analysis, and pattern searching. The program also supports the assembly of a set of contiguous sequences, consensus sequence generation, and sequence similarity and conservancy analysis. FastPCR performs efficient and complete detection of various repeat types with visual display. FastPCR allows for sequence file batch processing that is essential for automation. The software is available for download at https://primerdigital.com/fastpcr.html and online version at https://primerdigital.com/tools/pcr.html.

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Acknowledgments

This work was supported by the company PrimerDigital Ltd. (Helsinki, Finland) and partly by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan (Grant No. AP08855353). The authors wish to thank Derek Ho (The University of Helsinki Language Centre) for editing and proofreading of the manuscript.

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Authors and Affiliations

  1. PrimerDigital Ltd, Biocentre 3, Helsinki, Finland

    Ruslan Kalendar

  2. National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan

    Ruslan Kalendar

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  1. Ruslan Kalendar
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Correspondence to Ruslan Kalendar .

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Editors and Affiliations

  1. Department of Biology, California State University, Northridge, Los Angeles, CA, USA

    Chhandak Basu

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Kalendar, R. (2022). A Guide to Using FASTPCR Software for PCR, In Silico PCR, and Oligonucleotide Analysis. In: Basu, C. (eds) PCR Primer Design. Methods in Molecular Biology, vol 2392. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1799-1_16

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  • DOI: https://doi.org/10.1007/978-1-0716-1799-1_16

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1798-4

  • Online ISBN: 978-1-0716-1799-1

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