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

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

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 programme 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, linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with GC 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 analyses 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
EditorsSvein Valla, Rahmi Lale
Number of pages32
Volume1116
Place of PublicationSpringer Science+Business Media, New York
PublisherHumana Press
Publication date2014
Pages271-302
ISBN (Print)978-1-62703-763-1
ISBN (Electronic)978-1-62703-764-8
DOIs
Publication statusPublished - 2014
MoE publication typeA3 Book chapter

Publication series

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

Fields of Science

  • 1182 Biochemistry, cell and molecular biology

Cite this

Kalendar, R., Lee, D., & Schulman, A. (2014). FASTPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. In S. Valla, & R. Lale (Eds.), DNA Cloning and Assembly Methods (Vol. 1116, pp. 271-302). (Methods in Molecular Biology; Vol. 1116). Springer Science+Business Media, New York: Humana Press. https://doi.org/10.1007/978-1-62703-764-8_18
Kalendar, Ruslan ; Lee, David ; Schulman, Alan. / FASTPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. DNA Cloning and Assembly Methods. editor / Svein Valla ; Rahmi Lale. Vol. 1116 Springer Science+Business Media, New York : Humana Press, 2014. pp. 271-302 (Methods in Molecular Biology).
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Kalendar, R, Lee, D & Schulman, A 2014, FASTPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. in S Valla & R Lale (eds), DNA Cloning and Assembly Methods. vol. 1116, Methods in Molecular Biology, vol. 1116, Humana Press, Springer Science+Business Media, New York, pp. 271-302. https://doi.org/10.1007/978-1-62703-764-8_18

FASTPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. / Kalendar, Ruslan; Lee, David; Schulman, Alan.

DNA Cloning and Assembly Methods. ed. / Svein Valla; Rahmi Lale. Vol. 1116 Springer Science+Business Media, New York : Humana Press, 2014. p. 271-302 (Methods in Molecular Biology; Vol. 1116).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

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AB - 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 programme 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, linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with GC 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 analyses 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.

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M3 - Chapter

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VL - 1116

T3 - Methods in Molecular Biology

SP - 271

EP - 302

BT - DNA Cloning and Assembly Methods

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PB - Humana Press

CY - Springer Science+Business Media, New York

ER -

Kalendar R, Lee D, Schulman A. FASTPCR software for PCR, in silico PCR, and oligonucleotide assembly and analysis. In Valla S, Lale R, editors, DNA Cloning and Assembly Methods. Vol. 1116. Springer Science+Business Media, New York: Humana Press. 2014. p. 271-302. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-62703-764-8_18