Our Plant Databases

Metabolomics -GC/MS, LC/MS, CE/MS ...
  1. PRIMe [Link]
    A Web site that assembles tools for metabolomics and transcriptomics
    Akiyama K. et al. In Silico Biology 8 339-345 (2008) [PubMed] [Link]
  2. PRIMeLink [Link]
    Innovative content for plant metabolomics and integration of gene expression and metabolite accumulation
    Sakurai S. et al. Plant Cell Physiology 54(2) e5(1-8) (2013) [PubMed] [Link]
  3. ReSpect [Link]
    A collection of literature and in-house MSn spectra data for research on plant metabolomics
    Sawada Y. et al. Phytochemistry 82 38-45 (2012) [PubMed] [Link]
  4. HIFI [Link]
    A tool for liquid chromatography-fourier transfer ion cyclotron resonance-mass spectrometry (LC-FTICR-MS)
Phenotype, Genomics -phenome, cDNA, mutant ...
  1. RARGE II [Link]
    An integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary
    Akiyama K. et al. Plant Cell Physiology 55(1) e4(1-10) (2014) [PubMed] [Link]
  2. RARGE [Link]
    A large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome
    Akiyama K. et al. Nucleic Acids Research 33:D647-650 (2005) [PubMed] [Link]
  3. The Chloroplast Function Database II [Link]
    A comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins
    Myouga F. et al. Plant Cell Physiology 54(2) e2(1-10) (2013) [PubMed] [Link]
  4. Cassava Online Archive [Link]
    Information resource of cassava for genetic improvement
    Sakurai T. et al. PLOS One 11 8(9) e74056 (2013) [PubMed] [Link]
  5. RIKEN Brachypodium FLcDNA database [Link]
    Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with pooideae sequence resources
    Mochida K. et al. PLOS One 8 10 e75265 (2013) [PubMed] [Link]
  6. UniVio [Link]
    A multiple omics database with hormonome and transcriptome data from rice
    Kudo T. et al. Plant Cell Physiology 54(2) e9(1-12) (2013) [PubMed] [Link]
  7. RiceFOX [Link]
    A database of Arabidopsis mutant lines overexpressing rice full-length cDNA
    Myouga F. et al. Plant Cell Physiology 54(2) 265-273 (2011) [PubMed] [Link]
  8. TriFLDB [Link]
    A database of clustered full-length coding sequences from triticeae with applications to comparative grass genomics
    Mochida K. et al. Plant Physiology 150(3) 1135-1146 (2009) [PubMed] [Link]
  9. rsoy [Link]
    Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library
    Umezawa T. et al. DNA Research 15 333-346 (2008) [PubMed] [Link]
  10. RAPID [Link]
    A trial of phenome analysis using 4000 Ds-insertional mutants in gene-coding regions of Arabidopsis
    Kuromori T. et al. Plant Journal 640-651 (2006) [PubMed] [Link]
  11. Alga-PrAS [Link]
    A database of physicochemical and structural properties and post-translational modifications in algal proteomes

Ohter Links

  1. DLP-SVM [Link]
    DLP-SVM is a prediction tool of protein domain linkers.
    Ebina T. et al. Biopolymers 92(1) 1-8 (2009) [PubMed] [Link]
  2. H-DROP [Link]
    H-DROP is a SVM based helical domain linker predictor for proteomics search.
    Ebina T. et al. J. Comput. Aided. Mol. Des. 28(8) 831-839 (2014) [PubMed] [Link]
  3. IS-Dom[Link]
    IS-Dom is a database of independent structural domains automatically delineated from protein structures.
    Ebina T. et al. J. Comput. Aided. Mol. Des. 27(5) 419-426 (2013) [PubMed] [Link]
▲ Page Top
Copyright © 2014- RIKEN
RIKEN RIKEN  | CSRS  | Integrated Genome Informatics Research Unit