SNP-Seek database Edit

Citations: 95

z-index: 23.75

Basic information
Short name SNP-Seek database
Full name SNP-Seek Database
Description SNP-Seek provides Genotype, Phenotype, and Variety Information for rice derived from 3,000 Rice Genomes Project.
Year founded 2014
Last update & version 2016-12-12 v1.0
Accessibility Accessible
Contact information

The contact information is provided to facilitate update of database information, and it is curated based on the contact details in the database or the related publications. To ensure effective contact with database constructors, we give priority to the contact details in the database.

University/Institution International Rice Research Institute
Address Los Ba–os,Laguna 4031,Philippines
City Los Ba–os
Province/State Laguna
Country/Region Philippines
Contact name (PI/Team) Nickolai Alexandrov
Contact email (PI/Helpdesk)
Data information
Data object
Data type
Database category
Major organism
  • Rice SNP-seek database update: new SNPs, indels, and queries. [PMID: 27899667]
    Locedie Mansueto, Roven Rommel Fuentes, Frances Nikki Borja, Jeffery Detras, Juan Miguel Abriol-Santos, Dmytro Chebotarov, Millicent Sanciangco, Kevin Palis, Dario Copetti, Alexandre Poliakov, Inna Dubchak, Victor Solovyev, Rod A Wing, Ruaraidh Sackville Hamilton, Ramil Mauleon, Kenneth L McNally, Nickolai Alexandrov

    We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

    Nucleic Acids Res 2017:45(D1)

    16 Citations (from Europe PMC, 2019-08-03)

  • SNP-Seek database of SNPs derived from 3000 rice genomes. [PMID: 25429973]
    Nickolai Alexandrov, Shuaishuai Tai, Wensheng Wang, Locedie Mansueto, Kevin Palis, Roven Rommel Fuentes, Victor Jun Ulat, Dmytro Chebotarov, Gengyun Zhang, Zhikang Li, Ramil Mauleon, Ruaraidh Sackville Hamilton, Kenneth L McNally

    We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (, which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs × 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

    Nucleic Acids Res 2015:43(Database issue)

    79 Citations (from Europe PMC, 2019-08-03)


  • Ranking in all databases: No. 301
  • Ranking in category/categories:
    • Genotype phenotype and variation: No. 39
The box plots depict Z-index distribution for all databases in Database Commons and for specific database category/categories. The red line indicates log2(Z-index) of SNP-Seek database.

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Record metadata

  • Created on: 2015-06-20
    • ***ng***ng@*** [2019-05-13]
    • ***ina@*** [2018-06-05]
    • ***shx@*** [2017-02-20]
    • ***lin@*** [2016-03-28]
    • ***engwei@*** [2016-02-18]
    • ***lin@*** [2015-11-20]
    • ***lin@*** [2015-06-28]
    • ***gj@*** [2015-06-26]

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