Rice SNP-Seek Database specifications


Unique identifier OMICS_06654
Name Rice SNP-Seek Database
Alternative name SNP-Seek Database
Restrictions to use None
Maintained No


  • Plants and Fungi
    • Oryza sativa


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Publications for Rice SNP-Seek Database

Rice SNP-Seek Database citations


Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice

PLoS One
PMCID: 5708779
PMID: 29190814
DOI: 10.1371/journal.pone.0188920

[…] Whole genome data for 3024 rice varieties were made available from the 3000 rice genome project [], which included 76 aromatic rice varieties. A searchable Rice SNP-Seek Database containing about 20 million SNPs obtained after aligning these genomes with the Nipponbare reference was created [] and further updated to include InDels []. Using this database […]


Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa)

PMCID: 5449364
PMID: 28560587
DOI: 10.1186/s12284-017-0164-3
call_split See protocol

[…] he intron boundaries were analyzed by Weblogo (http://weblogo.berkeley.edu/logo.cgi).Single nucleotide polymorphisms (SNP) in the EUL genes between different rice subspecies were identified using the SNP-Seek database containing SNP genotyping data (called against Nipponbare reference Os-Nipponbare-Reference-IRGSP-1.0) from the 3000 Rice Genomes Project (Alexandrov et al. ). The use of the Nipponb […]

Rice SNP-Seek Database institution(s)
TTChang Genetic Resources Center, IRRI, Los BaƱos, Laguna, Philippines; BGI, Shenzhen, China; Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
Rice SNP-Seek Database funding source(s)
Supported by the Global Rice Science Partnership (GRiSP), the Bill and Melinda Gates Foundation (OPPGD1393), International S&T Cooperation Program of China (2012DFB32280) and the Peacock Team Award to ZLI from the Shenzhen Municipal government.

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