FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis

Ruslan Kalendar; Bekbolat Khassenov; Yerlan Ramankulov; Olga Samuilova; Konstantin I Ivanov

doi:10.1016/j.ygeno.2017.05.005

FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis

Genomics. 2017 Jul;109(3-4):312-319. doi: 10.1016/j.ygeno.2017.05.005. Epub 2017 May 12.

Authors

Ruslan Kalendar¹, Bekbolat Khassenov², Yerlan Ramankulov³, Olga Samuilova⁴, Konstantin I Ivanov⁵

Affiliations

¹ PrimerDigital Ltd, FIN-00710 Helsinki, Finland. Electronic address: ruslan.kalendar@primerdigital.com.
² RSE "National Center for Biotechnology" under the Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Astana, Kazakhstan. Electronic address: khassenov@biocenter.kz.
³ RSE "National Center for Biotechnology" under the Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Astana, Kazakhstan. Electronic address: ramanculov@biocenter.kz.
⁴ Department of Biochemistry, I.M. Sechenov First Moscow State Medical University, 8-2 Trubetskaya st., Moscow 119991, Russian Federation.
⁵ Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119234, Russian Federation.

PMID: 28502701
DOI: 10.1016/j.ygeno.2017.05.005

Abstract

Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability. The software determines primer location, orientation, efficiency of binding and calculates primer melting temperatures for standard and degenerate oligonucleotides. The software is suitable for batch file processing, which is essential for automation when working with large amounts of data. The online Java software is available for download at http://primerdigital.com/tools/pcr.html. Accession numbers for the sequences resulting from this study: EU140956 EU177767 EU867815 EU882730 FJ975775-FJ975780 HM481419 HM481420 KC686837-KC686839 KM262797.

Keywords: DNA fingerprinting; DNA primers; Degenerate PCR; Genetic engineering tools; Isothermal amplification of nucleic acids; Nucleic acid hybridization; PCR primer and probe analysis; Polymerase chain reaction; Primer binding site; Probe.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computer Simulation*
DNA Primers*
DNA Probes
Polymerase Chain Reaction / methods*
Sequence Analysis, DNA / methods*
Software*

Substances

DNA Primers
DNA Probes