Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis

Research output: Contribution to journalArticleScientificpeer-review

Abstract

The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict properties oligonucleotides based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by 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-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.
Original languageEnglish
JournalGenomics
Volume98
Issue number2
Pages (from-to)137-144
Number of pages8
ISSN0888-7543
DOIs
Publication statusPublished - 2011
MoE publication typeA1 Journal article-refereed

Fields of Science

  • PCR primer design
  • Primer linguistic complexity
  • Sequence assembly
  • Software
  • Probe design
  • Ligase chain reaction
  • NEAREST-NEIGHBOR THERMODYNAMICS
  • POLYMERASE-CHAIN-REACTION
  • PRIMER DESIGN
  • SEQUENCE COMPLEXITY
  • GENE SYNTHESIS
  • DNA DUPLEXES
  • POLYMORPHISMS
  • MISMATCHES
  • EXTENSION
  • GENOMES
  • 113 Computer and information sciences
  • 1184 Genetics, developmental biology, physiology

Cite this

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title = "Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis",
abstract = "The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict properties oligonucleotides based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by 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-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.",
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author = "Ruslan Kalendar and David Lee and Schulman, {Alan H.}",
year = "2011",
doi = "10.1016/j.ygeno.2011.04.009",
language = "English",
volume = "98",
pages = "137--144",
journal = "Genomics",
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}

Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. / Kalendar, Ruslan; Lee, David; Schulman, Alan H.

In: Genomics, Vol. 98, No. 2, 2011, p. 137-144.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

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AU - Lee, David

AU - Schulman, Alan H.

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AB - The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict properties oligonucleotides based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by 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-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.

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