In silico PCR tools for a fast primer, probe, and advanced searching

Ruslan Kalendar, Alexandr Muterko, Malika Shamekova, Kabyl Zhambakin

Research output: Chapter in Book/Report/Conference proceedingChapter

19 Citations (Scopus)


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 and the online Java version at

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages31
Publication statusPublished - 2017
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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