News


3K RG 1M GWAS SNP Dataset available for download in SNP-Seek

posted Oct 23, 2017, 8:09 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Oct 23, 2017, 11:19 PM ]

    New LD pruned subset to try for GWAS is available as downloadable dataset in snp-seek. The data is based on the
Filtered SNP set (4.8M), a subset of Base SNP (18M). It was done with one round of LD pruning, r2 cutoff 0.8, window size
2kb and step 1 SNP, to remove only SNPs that are less than ~2kb apart. This leaves 1, 011, 601 snps.

    Visit our Bulk Download Page, scroll down and look for 3K RG 1M GWAS SNP Dataset, all chromosomes.

Haplotype view available in SNP-Seek

posted Jul 31, 2017, 7:38 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Aug 1, 2017, 12:50 AM ]

A new feature in SNP-Seek that will make snp mining easier and more fun is made available. Haplotype view is here.

Just visit snp-seek.irri.org and make a query in genotype search and choose the Haplotype view as shown below.



The haplotype view allows user to cluster and visualize the genotype groups of varieties.


Salinity phenotype data available in SNP-seek

posted Jul 9, 2017, 8:03 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Jul 9, 2017, 8:47 PM ]

Dr. RK Singh's team evaluated response to salinity stress measured for electrical conductivity at 12 dS/m and 18 dS/m during seedling stage for 1,999 genomes from 3Krg dataset. The data is labeled as “salt injury” in the SNP-seek database.

SNP-Seek USE CASE: Get variations in a region

posted Apr 6, 2017, 1:39 AM by Frances Nikki Borja ‎(IRRI)‎

A. Given a region of interest (gene), get similar varieties


Region of interest: LOC_Os04g57530


  1. Go to Genotype search page

  2. Supply the known information. Choose all varieties in the multiple: Subpopulation drop down menu in the Compare Varieties section. Supply the gene locus id in the Gene locus query box in the Region section.




  3. The table matrix showing the accession with variation in the region will be returned. There are 78 varieties that shown variation in this region. The table matrix is downloaded in CSV to further examine the region.


  4. Results can be downloaded as CSV format by clicking the CSV box in the Download section.




For more use cases visit our Help page.

IRIC Workshop at PAG XXV

posted Jan 4, 2017, 7:29 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Jan 5, 2017, 5:10 PM ]

The IRIC Workshop will be held on 18 January 2017 at Plant and Animal Genome Conference XXV in San Diego, California.
Talks will be given by Nickolai Alexandrov, David Edwards, Dario Copetti, Pierre Larmande, Tatiana Tatarinova and Jeremy Edwards. The talks are:

International Rice Informatics Consortium: 3,000 Rice Genomes Explorations and Beyond

Nickolai Alexandrov, International Rice Research Institute, Los Baños, Philippines

Development of WheatIS and Collaboration between Plant Information System

Chon-Kit Kenneth Chan1, Philipp E. Bayer1, Robert P. Davey2, Michael Alaux3, Cyril Pommier3, Hadi Quesneville3, Mario J Caccamo4, Gerard R. Lazo5, Kenneth L. McNally6, Nickolai Alexandrov6 and David Edwards1, (1)University of Western Australia, Perth, Australia, (2)Earlham Institute, Norwich, United Kingdom, (3)INRA - URGI, Versailles, France, (4)NIAB, Cambridge, United Kingdom, (5)USDA Agricultural Research Service, WRRC, Albany, CA, (6)International Rice Research Institute, Los Baños, Philippines

Development of Gap-Free Genome Assemblies to Capture and Exploit Rice Genetic Variation

Dario Copetti1, David Kudrna1, Jianwei Zhang1, Kenneth L. McNally2, Nickolai Alexandrov2, Ramil P. Mauleon2 and Rod Wing3, (1)Arizona Genomics Institute, Tucson, AZ, (2)International Rice Research Institute, Los Baños, Philippines, (3)School of Plant Sciences, Ecology & Evolutionary Biology, Arizona Genomics Institute, Tucson, AZ

The Rice Data Interoperability Working Group

Pierre Larmande, IRD, UMR DIADE, Institut de Biologie Computationnelle, Montpellier, France, Ramil P. Mauleon, International Rice Research Institute, Los Baños, Philippines, Shaik N.M. N.Meera, Indian Institute of Rice Research (IIRR), Hyderabad, India, Imma S. Subirats, FAO, Rome, Italy and Devika M. Madalli, Indian Statistical Institute, Kolkata, India

Genome-Wide Analysis of SNPs in Promoter Regsions of Oryza sativa

Tatiana Tatarinova1, Victor Solovyev2, Kenneth L. McNally3 and Nickolai Alexandrov3, (1)University of Southern California, Los Angeles, CA, (2)Softberry, Mount Kisco, NY, (3)International Rice Research Institute, Los Baños, Philippines

Ricebase - a Resource for Rice Breeding

Jeremy D. Edwards, USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR


Locedie Mansueto, a developer from IRRI, will deliver a demonstration about the features of SNP-Seek on the same day at 11:00 a.m and present the scientific poster SNP-Seek Resource for Rice Research.

IR8

posted Dec 21, 2016, 7:57 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Dec 21, 2016, 10:43 PM ]

As we celebrate the 50th anniversary of the official release of IR8, we are pleased to announce the availability of IR8's high quality genome assembly, using whole genome shotgun sequencing. The semidwarf rice variety is considered as miracle rice for it is believed to have saved Asia from famine during the late 1960s.

The IR8 sequence and assembly are available at NCBI.

You can read more about IR8, its conception, history and many more at irri website.

New Feature released

posted Nov 9, 2016, 9:16 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Nov 9, 2016, 9:18 PM ]

Another feature has been added to further assist you in your snp-seeking. Searching across the 3K panel for similar accession to particular accession is now possible.

Choose the accession of interest as reference for the rest of the 3k panel by choosing the Accession in the variety drop down menu in the Region section.

Visit our online rice snp-seek database at http://snp-seek.irri.org.



SNP Seek is moving to snp-seek.irri.org

posted Sep 19, 2016, 11:51 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Sep 20, 2016, 12:04 AM ]

In our efforts to make our website address shorter and easier to remember, we are pleased to announce the new website address of SNP Seek.
You may access SNP Seek at http://snp-seek.irri.org/. SNP Seek may still be accessed using the old website address (http://oryzasnp.org/iric-portal) until November 2016.

HDRA available in SNPSeek

posted Jul 26, 2016, 1:20 AM by Frances Nikki Borja ‎(IRRI)‎

High Density Rice Array (HDRA) data is now available in SNP Seek Portal.

http://oryzasnp.org/iric-portal/

Genome Sequence of N 22 Available

posted May 30, 2016, 7:41 PM by Frances Nikki Borja ‎(IRRI)‎   [ updated Sep 13, 2017, 9:16 PM ]

    Through collaboration by IRRI and the Arizona Genomics Institute, a RefSeq quality genome build for the aus N 22 was recently completed using the whole genome shotgun approach with PacBio sequencing technology.  The predicted error rate is on par with that of Nipponbare (<1 error per 10,000 bases).
     N22 is important for several reasons:  it is heat and drought tolerant, deep-rooted and the source of a number of resources for functional genomics. 
    The genome assembly has been uploaded to Genbank with accession number LWDA00000000. Gene annotation was done using the Maker-P pipeline, with final annotation of TE genes in process.  Chloroplast and mitochondrial assemblies are also available for this build.

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