FastPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis

Ruslan Kalendar, David Lee, Alan H. Schulman

Research output: Chapter in Book/Report/Conference proceedingChapter

66 Citations (Scopus)

Abstract

This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a program to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, and linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with CG or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyzes sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and online version at http://primerdigital.com/tools/pcr.html.

Original languageEnglish
Title of host publicationDNA Cloning and Assembly Methods
PublisherHumana Press Inc.
Pages271-302
Number of pages32
ISBN (Print)9781627037631
DOIs
Publication statusPublished - 2014

Publication series

NameMethods in Molecular Biology
Volume1116
ISSN (Print)1064-3745

Keywords

  • DNA primers
  • Ligase chain reaction
  • PCR primer design
  • Primer linguistic complexity
  • Sequence assembly
  • Software probe design

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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