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Database Commons - RGKbase

RGKbase

Citations: 9

z-index 0.88

Short name RGKbase
Full name Rice Genome Knowledgebase
Description An annotation database for rice comparative genomics and evolutionary biology
URL http://rgkbase.big.ac.cn/RGKbase/
Year founded 2012
Last update & version 6/28/2012    v1.0
Availability Free to all users
University/Institution hosted Beijing Institute of Genomics, Chinese Academy of Sciences
Address Beijing 100029,China
City Beijing
Province/State
Country/Region China
Contact name Jun Yu
Contact email junyu@big.ac.cn
Data type(s)
Major organism(s)
Keyword(s)
  • 93-11
  • nipponbare
Publication(s)
  • The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. [PMID: 23193278]

    Dapeng Wang, Yan Xia, Xinna Li, Lixia Hou, Jun Yu
    Nucleic acids research 2013:41(Database issue)
    9 Citations (Google Scholar as of 2016-04-25)

    Abstract: Over the past 10 years, genomes of cultivated rice cultivars and their wild counterparts have been sequenced although most efforts are focused on genome assembly and annotation of two major cultivated rice (Oryza sativa L.) subspecies, 93-11 (indica) and Nipponbare (japonica). To integrate information from genome assemblies and annotations for better analysis and application, we now introduce a comparative rice genome database, the Rice Genome Knowledgebase (RGKbase, http://rgkbase.big.ac.cn/RGKbase/). RGKbase is built to have three major components: (i) integrated data curation for rice genomics and molecular biology, which includes genome sequence assemblies, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and the relevant literature; (ii) User-friendly viewers, such as Gbrowse, GeneBrowse and Circos, for genome annotations and evolutionary dynamics and (iii) Bioinformatic tools for compositional and synteny analyses, gene family classifications, gene ontology terms and pathways and gene co-expression networks. RGKbase current includes data from five rice cultivars and species: Nipponbare (japonica), 93-11 (indica), PA64s (indica), the African rice (Oryza glaberrima) and a wild rice species (Oryza brachyantha). We are also constantly introducing new datasets from variety of public efforts, such as two recent releases-sequence data from ?1000 rice varieties, which are mapped into the reference genome, yielding ample high-quality single-nucleotide polymorphisms and insertions-deletions.

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200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

DNA
Oryza brachyantha Oryza glaberrima Oryza sativa
93-11 nipponbare

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Xia [2016-04-01]
    • Mengwei Li [2016-02-19]
    • Lin Xia [2015-11-23]
    • Lin Xia [2015-06-26]
Stats