Araport

Araport web portal is a comprehensive Arabidopsis thaliana genomics resource containing data mining and analysis tools (ThaleMine), JBrowse for genome exploration, genome context viewer, and community apps.

Topic

Genomics;Genotype and phenotype

Detail

  • Operation: Indexing;Query and retrieval

  • Software interface: Database portal;Web service

  • Language: -

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: CAGEF, University of Toronto, The Arabidopsis Information Resource, Phoeni, National Center For Genome Resources, J. Craig Venter Institute, University of Cambridge, Biotechnology and Biological Sciences Research Counsil, NSF

  • Input: -

  • Output: -

  • Contact: araport@jcvi.org

  • Collection: -

  • Maturity: Mature

Publications

  • Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny
  • Cleary A, Farmer A. Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny. Bioinformatics. 2018 May 1;34(9):1562-1564. doi: 10.1093/bioinformatics/btx757. PMID: 29194466; PMCID: PMC5925771.
  • https://doi.org/10.1093/bioinformatics/btx757
  • PMID: 29194466
  • PMC: PMC5925771
  • Araport: the Arabidopsis information portal
  • Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, Vaughn M, Town CD. Araport: the Arabidopsis information portal. Nucleic Acids Res. 2015 Jan;43(Database issue):D1003-9. doi: 10.1093/nar/gku1200. Epub 2014 Nov 20. PMID: 25414324; PMCID: PMC4383980.
  • https://doi.org/10.1093/nar/gku1200
  • PMID: 25414324
  • PMC: PMC4383980
  • Araport Lives: An Updated Framework for Arabidopsis Bioinformatics
  • Pasha A, Subramaniam S, Cleary A, Chen X, Berardini T, Farmer A, Town C, Provart N. Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. Plant Cell. 2020 Sep;32(9):2683-2686. doi: 10.1105/tpc.20.00358. Epub 2020 Jul 22. PMID: 32699173; PMCID: PMC7474289.
  • https://doi.org/10.1105/tpc.20.00358
  • PMID: 32699173
  • PMC: PMC7474289
  • Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.
  • Cheng CY, et al. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. 2017; 89:789-804. doi: 10.1111/tpj.13415
  • https://doi.org/10.1111/tpj.13415
  • PMID: 27862469
  • PMC: -

Download and documentation

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