U.S. flag

An official website of the United States government

The Ag Data Commons is migrating

The Ag Data Commons is migrating to a new institutional portal on Figshare. The current system is available for search and download only. The new platform is open for submission with assistance from Ag Data Commons curators. Please contact NAL-ADC-Curator@usda.gov, if you need to publish or update your datasets.

License

U.S. Public Domain
[Open Data]

Other Access

The information on this page (the dataset metadata) is also available in these formats:

JSON RDF

via the DKAN API

Social

CottonGen Primer3

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.

See all >>
FieldValue
Tags
CottonGen
np301
Primer3
Parent Record
CottonGen: Cotton Database Resources
Modified
2022-09-28
Release Date
2019-08-15
Identifier
4a131184-c0cb-4ec0-8429-b6e26c5596b9
Publisher
MainLab, Washington State University
License
U.S. Public Domain
Contact Name
Main, Dorrie
Contact Email
dorrie@wsu.edu
Public Access Level
Public
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service
Extended Metadata: 
FieldValue
Authors
Lee, Taein (ORCID)
Jung, Sook (Scopus Author ID)
Gasic, Ksenija (ORCID)
Campbell, Todd (ORCID)
Yu, Jing (Scopus Author ID)
Humann, Jodi (ORCID)
Hough, Heidi (Scopus Author ID)
Main, Dorrie (ORCID)
Peer Reviewed
No
Intended Use
Primer3web version 4.0.0 allows users to pick PCR primers from a DNA sequence.
Equipment or Software Used
Tripal infrastructure
Funding Sources
Cotton Incorporated
Agricultural Research Service
Crop Germplasm Research Unit, College Station, TX
Bayer CropScience
Dow Chemical Company
Monsanto Company
Washington State University
National Institute of Food and Agriculture
2009-51181-06036
National Institute of Food and Agriculture
2009-51181-05808
Primary Article

Yu, J., Jung, S., Cheng, C.-H., Ficklin, S. P., Lee, T., Zheng, P., Jones, D., Percy, R. G., & Main, D. (2013). CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Research, 42(D1), D1229-D1236. https://doi.org/10.1093/nar/gkt1064
Related Articles

Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3—new capabilities and interfaces. Nucleic Acids Research, 40(15), e115-e115. https://doi.org/10.1093/nar/gks596

Yu, J., Jung, S., Cheng, C.-H., Lee, T., Zheng, P., Buble, K., Crabb, J., Humann, J., Hough, H., Jones, D., Campbell, J. T., Udall, J., & Main, D. (2021). CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. Plants, 10(12), 2805. https://doi.org/10.3390/plants10122805

AgID: 7608357
Product Type
Dataset
Related Content
Primer3web - Help
FieldValue
ISO Topic(s)
biota
farming
National Agricultural Library Thesaurus Term
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
Ag Data Commons Keywords
  • Plants & Crops
  • Traits
  • Genomics & Genetics
  • Online database
  • Plants & Crops

Suggested Citations:

(original article) Yu, J., Jung, S., Cheng, C.-H., Ficklin, S. P., Lee, T., Zheng, P., Jones, D., Percy, R. G., & Main, D. (2013). CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Research, 42(D1), D1229-D1236. https://doi.org/10.1093/nar/gkt1064

(dataset) Lee, Taein; Jung, Sook; Gasic, Ksenija; Campbell, Todd; Yu, Jing; Humann, Jodi; Hough, Heidi; Main, Dorrie (2019). CottonGen Primer3. MainLab, Washington State University. https://data.nal.usda.gov/dataset/cottongen-primer3. Accessed 2023-12-10.