PCR pp 33-64 | Cite as

Introduction on Using the FastPCR Software and the Related Java Web Tools for PCR and Oligonucleotide Assembly and Analysis

  • Ruslan Kalendar
  • Timofey V. Tselykh
  • Bekbolat Khassenov
  • Erlan M. Ramanculov
Part of the Methods in Molecular Biology book series (MIMB, volume 1620)

Abstract

This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP). It also contains a built-in program to design oligonucleotide sets both for long sequence assembly by ligase chain reaction and for design of amplicons that tile across a region(s) of interest. The software calculates the melting temperature for the standard and degenerate oligonucleotides including locked nucleic acid (LNA) and other modifications. It also provides analyses for a set of primers with the prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity as well as a primer dilution and resuspension calculator. The program consists of various bioinformatical tools for analysis of sequences with the GC or AT skew, CG% and GA% content, and the purine–pyrimidine skew. It also analyzes the linguistic sequence complexity and performs generation of random DNA sequence as well as restriction endonucleases analysis. The program allows to find or create restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It performs efficient and complete detection of various repeat types with visual display. The FastPCR software allows the sequence file batch processing that is essential for automation. The program is available for download at http://primerdigital.com/fastpcr.html, and its online version is located at http://primerdigital.com/tools/pcr.html.

Key words

PCR primer design Isothermal amplification of nucleic acids Software probe design DNA primers DNA primers nucleic acid hybridization Degenerate PCR Tiling arrays Primer linguistic complexity Ligase chain reaction 

Notes

Acknowledgments

Web tools are available free, provided for noncommercial research and education use only. They may not be reproduced or distributed for commercial use. This work was supported by the companies PrimerDigital Ltd.

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Ruslan Kalendar
    • 1
    • 5
  • Timofey V. Tselykh
    • 2
    • 3
  • Bekbolat Khassenov
    • 4
  • Erlan M. Ramanculov
    • 4
  1. 1.National Center for BiotechnologyAstanaKazakhstan
  2. 2.Biochemistry and Developmental Biology, MedicumUniversity of HelsinkiHelsinkiFinland
  3. 3.Minerva Medical Research InstituteHelsinkiFinland
  4. 4.National Center for Biotechnology,AstanaKazakhstan
  5. 5.PrimerDigital LtdHelsinkiFinland

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