Introduction on using the FastPCR software and the related Java web tools for PCR and oligonucleotide assembly and analysis

Ruslan Kalendar, Timofey V. Tselykh

Research output: Chapter in Book/Report/Conference proceedingChapter

16 Citations (Scopus)

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.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages33-64
Number of pages32
DOIs
Publication statusPublished - 2017
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1620
ISSN (Print)1064-3745

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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