PCR pp 1-31 | Cite as

In Silico PCR Tools for a Fast Primer, Probe, and Advanced Searching

  • Ruslan Kalendar
  • Alexandr Muterko
  • Malika Shamekova
  • Kabyl Zhambakin
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1620)

Abstract

The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory “wet bench” experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching. Predicting sensitivity and specificity of primers and probes requires a search to determine whether they match a database with an optimal number of mismatches, similarity, and stability. In the development of in silico bioinformatics tools for nucleic acid amplification technologies, the prospects for the development of new NAAT or similar approaches should be taken into account, including forward-looking and comprehensive analysis that is not limited to only one PCR technique variant. The software FastPCR and the online Java web tool are integrated tools for in silico PCR of linear and circular DNA, multiple primer or probe searches in large or small databases and for advanced search. These tools are suitable for processing of batch files that are essential for automation when working with large amounts of data. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and the online Java version at http://primerdigital.com/tools/pcr.html.

Key words

Polymerase chain reaction Isothermal amplification of nucleic acids DNA primers nucleic acid hybridization Primer binding site PCR primer and probe analysis Degenerate PCR Probe Genetic engineering tools DNA fingerprints 

Notes

Acknowledgments

Java Web tools are publicly available. They may not be reproduced or distributed for commercial use. This work was supported by the companies Primer Digital Ltd.

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Ruslan Kalendar
    • 1
    • 4
  • Alexandr Muterko
    • 2
  • Malika Shamekova
    • 3
  • Kabyl Zhambakin
    • 3
  1. 1.National Center for BiotechnologyAstanaKazakhstan
  2. 2.Laboratory of Plant Molecular Genetics and CytogeneticsThe Federal Research Center Institute of Cytology and GeneticsNovosibirskRussia
  3. 3.Institute of Plant Biology and BiotechnologyAlmatyKazakhstan
  4. 4.PrimerDigital LtdHelsinkiFinland

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