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

Genomics
Ruslan KalendarKonstantin I Ivanov

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.

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Citations

Oct 3, 2017·Bioinformatics·Martin Christen Frølund ThomsenOle Lund
Jan 13, 2019·Applied and Environmental Microbiology·Benoit PaixStéphan Jacquet
Jan 11, 2020·Molecular Biology Reports·Marwa GhonaimAlan H Schulman
Oct 17, 2019·Frontiers in Behavioral Neuroscience·Olinda AlmeidaRui F Oliveira
Dec 14, 2019·Applications in Plant Sciences·Mark A Chapman
Apr 26, 2020·International Journal of Molecular Sciences·Ruslan KalendarAlan H Schulman
Jan 1, 2018·Functional Plant Biology : FPB·Ruslan KalendarAsset Daniyarov
Dec 19, 2019·Scientific Reports·Rick ConzemiusIvan Barišić
Jan 7, 2021·Applied Microbiology and Biotechnology·Iuliia Branco, Altino Choupina
Nov 19, 2020·Journal, Genetic Engineering & Biotechnology·Prosper Obed ChukwuemekaOyeyemi Janet Oretade
Jan 1, 2021·Biology Methods and Protocols·Oluwawemimo Adebowale, Liam Good
Feb 23, 2021·Ecology and Evolution·Ryan WimblesKirsty J Shaw
May 18, 2020·Journal of Virological Methods·Tey Putita OuVeasna Duong
Apr 22, 2021·Virus Genes·Vahid HasanvandArvind Varsani
Aug 21, 2020·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Timokratis KaramitrosAndreas Mentis
Apr 21, 2021·Molecular and Cellular Probes·Soha Seyyedi AbhariFarzad Badmasti
Nov 2, 2021·Frontiers in Bioengineering and Biotechnology·Yi YangHongwu Ma
Nov 20, 2021·International Journal of Systematic and Evolutionary Microbiology·Pieter-Jan KerkhofKurt Houf
Jul 30, 2021··Marie HoffmannKnut Reinert

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