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CottonGen Primer3

posted on 2024-02-13, 13:45 authored by Taein Lee, Sook Jung, Ksenija Gasic, Todd Campbell, Jing Yu, Jodi Humann, Heidi Hough, Dorrie Main

Primer3web version 4.0.0 allows users to pick PCR primers from a DNA sequence based on criteria including:

  • oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities,

  • PCR product size,

  • positional constraints within the source (template) sequence, and

  • possibilities for ectopic priming (amplifying the wrong sequence)

  • many other constraints.

All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair.

Resources in this dataset:


Cotton Incorporated

USDA-ARS: Crop Germplasm Research Unit, College Station, TX

Bayer CropScience

Dow Chemical Company

Monsanto Company

Washington State University

USDA-NIFA: 2009-51181-06036

USDA-NIFA: 2009-51181-05808


Data contact name

Main, Dorrie

Data contact email


MainLab, Washington State University

Intended use

Primer3web version 4.0.0 allows users to pick PCR primers from a DNA sequence.


  • Not specified

ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

Internet; databases; genomics; breeding; translation (genetics); applied research; cotton; infrastructure; quantitative trait loci; pathogens; germplasm conservation; pedigree; unigenes; expressed sequence tags; loci; taxonomy; germplasm; Gossypium; genetic markers; publications; genetic databases; plant breeding; plant genetics; computer software; genotype; genome; transcriptome; nucleotide sequences; DNA primers; polymerase chain reaction

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 301

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Lee, Taein; Jung, Sook; Gasic, Ksenija; Campbell, Todd; Yu, Jing; Humann, Jodi; Hough, Heidi; Main, Dorrie (2019). CottonGen Primer3. MainLab, Washington State University.

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