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CottonGen CottonCyc Pathways Database

dataset
posted on 2023-12-18, 18:09 authored by Taein Lee, Sook Jung, Ksenija Gasic, Todd Campbell, Jing Yu, Jodi Humann, Heidi Hough, Dorrie Main

The CottonGen CottonCyc Pathways Database, part of CottonGen, supports searching and browsing the following CottonCyc databases:

  • Cyc pathways for JGI v2.0 G. raimondii D5 genome assembly

This Cyc database was constructed using PathwayTools version 20.0 using the gene models from the JGI v2.0 D5 genome assembly of Gossypium raimondii. There has been no manual curation of this Cyc database. Pathway predictions were made using PathwayTools and in-silico v2.1 annotations as provided by JGI.

  • Cyc pathways for CGP-BGI v1.0 G. hirsutum AD1 genome assembly

This Cyc database was constructed using PathwayTools version 20.0 using the gene models from the CGP-BGI v1.0 AD1 genome assembly of Gossypium hirsutum. There has been no manual curation of this Cyc database. Pathway predictions were made using PathwayTools and in-silico v1.0 annotations as provided by CGP-BGI.

Search parameters include genes, proteins, RNAs, compounds, reactions, pathways, growth media, and BLAST search.


Resources in this dataset:

Funding

Cotton Incorporated

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

Bayer CropScience

Dow Chemical Company: Phytogen

Monsanto Company

Washington State University

USDA-NIFA: 2009-51181-06036

USDA-NIFA: 2009-51181-05808

History

Data contact name

Main, Dorrie

Data contact email

dorrie@wsu.edu

Publisher

MainLab, Washington State University

Theme

  • Not specified

ISO Topic Category

  • biota

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 raimondii; genetic markers; publications; genetic databases; plant breeding; plant genetics; computer software; genotype

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 CottonCyc Pathways Database. MainLab, Washington State University.

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    Categories

    Keywords

    CottonGenCottonDBCotton Marker DatabaseTripal databaseGBrowseCMapNCBI BLASTNP301Online databasedata.govARS

    Licence

    U.S. Public Domain

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