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Database Commons - SNP-Seek database

SNP-Seek database

Citations: 53

z-index 9.54

Short name SNP-Seek database
Full name SNP-Seek Database
Description This site provides Genotype,Phenotype,and Variety Information for rice
URL http://www.oryzasnp.org/iric-portal/
Year founded 2014
Last update & version 2016-12-12    v1.0
Availability Free to all users
University/Institution hosted International Rice Research Institute
Address Los Ba–os,Laguna 4031,Philippines
City Los Ba–os
Province/State Laguna
Country/Region Philippines
Contact name Nickolai Alexandrov
Contact email n.alexandrov@irri.org
Data type(s)
Major organism(s)
Keyword(s)
  • genotype
  • phenotype
  • snp
Publication(s)
  • 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
    Nucleic acids research 2017:45(D1)
    1 Citations (Google Scholar as of 2017-02-20)

    Abstract: 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: http://snp-seek.irri.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • 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
    Nucleic acids research 2015:43(Database issue)
    52 Citations (Google Scholar as of 2017-02-20)

    Abstract: 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 (http://www.oryzasnp.org/iric-portal/), 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.

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200 OK2016-12-23
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200 OK2016-12-13
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200 OK2016-11-11
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200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
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200 OK2016-04-15
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200 OK2016-04-08
200 OK2016-04-05
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200 OK2016-03-21
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200 OK2016-03-07
200 OK2016-03-04
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200 OK2016-02-19
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200 OK2016-02-15
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200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
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200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
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200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
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 Phenotype
Oryza sativa
genotype phenotype snp

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Shixiang Sun [2017-02-20]
    • Lin Xia [2016-03-28]
    • Mengwei Li [2016-02-18]
    • Lin Xia [2015-11-20]
    • Lin Xia [2015-06-28]
    • Jian Sang [2015-06-26]
Stats