About this site

This site provides Genotype, Phenotype, and Variety Information for rice (Oryza sativa L.). SNP genotyping data (called against Nipponbare reference Os-Nipponbare-Reference-IRGSP-1.0) came from 3,000 Rice Genomes Project . Phenotype and passport data for the 3,000 rice varieties came from the International Rice Genebank Collection Information System (IRGCIS). We are a part of an ongoing effort by the International Rice Informatics Consortium (IRIC) to centralize information access to rice research data and provide computational tools to facilitate rice improvement via discovery of new gene-trait associations and accelerated breeding.

How to Cite SNP-Seek

Primary publication

Other publications

Updates log

9/4/2020

• UPDATE: (Galaxy Tab) Removed IP address of galaxy instance in the display.

7/22/2020

• UPDATE: (Seed Ordering) Changed seed ordering link from snp-seek to irri.org seed resounces link.
• UPDATE: (Genotype Search) Removed the first line in the CSV downloadable version in search genotype.
• FIXED: (Haplotype Tab) Haplotype Viewer for other organism

6/24/2020

• FIXED: (Haplotype View) Update geno_heatmap.R to address issue of randomness for every refresh of page in haplotype viewer.

6/4/2020

• FIXED: Genotype Search query using user's variety and locus list

5/13/2020

• UPDATE: (Report Bugs) Added scanning multiple submitted images for virus.
• ADD: FAQ page.
• ADDED: (Sequence Download) Pop up message informing user about the 3k repository as alternative for bulk download.

4/22/2020

• UPDATE: (Bug Report) Added send/post/add multiple images.

3/31/2020

• ADDED: (Bug report) Updated the link use by SNP-seek
• UPDATED: (Gene Loci Search) Fixed Search by Gene Set/Networks Using Users' list (locus)
• FIXED: (Galaxy Tab) Resolved exception when no workflow is selected in Galaxy download tab under Genotype Search
• ADDED: (Search Genotype) Enable users to select multiple dataset in queries

3/24/2020

• UPDATE: (Search Genotype) Limit selection to Nipponbarre.

3/17/2020

• UPDATE: A docker image containing 3kFiltered dataset is deployed publicly in docker hub. This image is built on top of postgresql docker image.

2/13/2020

• Deployed SNP-seek(version 5.4.0) with the ff. updates
• UPDATE: Removed "all" option of variety selection in download section
• ADDED: ZK Charts license Agreement for development

1/27/2020

• BUG FIXED: "Add Filter" in genotype results

12/18/2019

• ADDED: "Open Source License Agreement" file in the project
• ADDED: A pop-up disclaimer message before downloading a sequence.
• BUG FIXED: URL object in galaxyFacade class that is use to refer to downloads in galaxy.

11/12/2019

• UPDATE: Fixed Download link for bulk files

10/28/2019

• UPDATE: Removed unused files
• ADDED: License file to Development Docs and in the menu
• ADDED: New folder for Documentations
• REMOVED: ZK charts in project that is publicly accessed or for redistribution purposes. Requiring external developers to get a license for ZK charts if they want to include charts.

10/21/2019

• UPDATE: Changed link of "Report Bugs" page

10/01/2019

• BUG FIXED: Searched genotype using Locus MyList
• BUG FIXED: Genotype search using NONSYNONYMOUS and a list from user

09/05/2019

• NEW: SNP-seek is now using HTTPS.
• UPDATE: Improve SNP effect tab user interface
• UPDATE: Chromosomes now sorted
• BUG FIXED: Error when querying genotype directly using non-synonymous option
• BUG FIXED: Empty MDS plot view in the results of Genotype Query
• BUG FIXED: Empty SNP effect table.
• BUG FIXED: Haplotype view error
• BUG FIXED: Download CSV file does not have Snp effect info
• BUG FIXED: Bug regarding downloading a big dataset
• BUG FIXED: Displaying of manhattan plot in GWAS tab
• BUG FIXED: Bugs in download page caused by the merging.
• BUG FIXED: Bugs in "Add Filter" feature in SNP genotype page (SNP seek)

06/03/2019

• UPDATE: Added Disclaimer note in the contactUS page
• BUG FIXED: Manhattan plot not displaying due to NullException when selecting SNP -log list

05/20/2019

• BUG FIXED: Resolve upload in MyList by updating jars used.
• UPDATE: Merge remote-tracking branch 'origin/temp-with-galaxy' into SnpSeekMavenProj. Resolved conflicting jars

05/16/2019

• UPDATE: Added exttab, galaxy pages. Exttab moved the tabpanels into a separate zul, allowing to be displayed in new window on right click of tabs. Galaxy submit long running computations into a galaxy instance using blend4j, bioblend and jython.Uses python library included in WEB-INF/lib/Lib
• UPDATE: right clickable tabs, Galaxy tab, vcf2fasta in galaxy-dev. Right clickable tabs, Galaxy tab, vcf2fasta in galaxy-dev http://13.250.4.164:8080

05/07/2019

• UPDATE: Change naming convention in property files
• UPDATE: Dockerfile to use updated docker image for the portal
• BUG FIXED: NullPointerException due to adding of filters
• ADDED: "dataset"" Attribute to VariantAlignmentTableArraysImpl class

12/05/2018

• UPDATE: Database schema has changed. ADDED: 'dataset' (String) in SnpAllVars object to make it more unique aside from retrieving VarId alone
• UPDATE: Changed Mapping Map(BigDecimal, StockSample) to Map(String, Map(BigDecimal, StockSample)) to display multiple dataset with similar samples
• UPDATE: ListItemsDAOAllImpl - remove if statement that handles one dataset. instead implemented it by retrieval by Set regardless how many dataset.
• UPDATE: Bug Fixed in displaying multiple dataset with similar samples
• ADDED: Dataset variable to IndelStringAllVarsImpl class and a new Mapping variable Variety to Dataset variable.

11/06/2018

• UPDATE: Project converted to a Maven project

10/16/2018

• ADDED: Legacy Web Services and usecases. GetAllCOTerms, GetCOTerm, GetAllCOTerms given a variety, Get Record by Variety and CO Term
• FIXED: "Download Error Message" in bulk download

10/10/2018

• FIXED: MDS PLOT error. snp-seek.irri.org/_variety.zul?irisid=allmds returns error 500

09/11/2018

• ADDED: "OS" tag to config file for setting values for OPERATING SYSTEM. This is to determine what HDF5 libraries are to be loaded.
• ADDED: defaultOrganism in the webserver config file to set initial value for organism.
• FIXED: Nullpointer for BigListBox in SNP Genotype tab.
• ADDED: dockerfile. This dockerfile deploys precompiled JAVA codes of snpseek portal to docker.

09/11/2018

• FIXED: NULL Pointer Exception blast servername.
• ADDED: filter for chr String, filtering whole word "Chromosome"
• UPDATE: Vscaddolds organism to retrieve name in getName method instead of getting the uniquename
• FIXED: "Processing icon" that locks the screen even an exception was thrown
• FIXED: Null pointer exception in GenotypeWS
• ADDED: New citation in the main page.
• ADDED: Info in the page regarding why other reference genomes are missing

08/01/2018

• UPDATE: Home Page. Added "How to Cite SNP seek.
• Fixed: BAM and VCF Download in the Download Page

07/16/2018

• UPDATE: Publication page content. Page format of this page was also changed.
• FIXED: BrAPI web services VAllStockBasicpropDaoImpl.
• ADDED: findVarietyByNamesLike and findVarietyById
• FIXED: findVarietiesByDataset. If all is selected, All varAllStock.

07/05/2018

• BrAPI web services: Fix applied to usecases like germplasmPUI, findVarietyByNamesLike when input dataset is set to "all".
• BrAPI web services: Implemented usecases findVAllstockBasicpropByNamesLikeDataset and findAllVAllstockBasicprops.

06/20/2018

• Added option to phenotype list (in Variety Tab) to viewed in legacy terms or as CO Terms.
• Removed case sensitivity to List Combo boxes e.g. Chromosome, Locus in Genotype Search and Sequence download page. And Designation, Accession, Assay Id in variety search.

05/16/2018

• Deployed new user-interface for SNP-Seek.
• Added "download as CSV" button to download GWAS results in CSV file format.
• Added Confirmation message after a successful creation of user defined list in Variety Search.
• Implemented findAllVariety which accepts a set of dataset and return a set of varieties.

02/03/2018

• Implemented an email service using AWS SES mailer to send seed orders.
• Set SNP Seek portal to use configuration files to toggle portal components' visibility.
• Developed new schema to easily add new datasets.
• Independent selection of dataset and SNP set.

12/01/2017

• Added page for seed orders from IRRI Genebank.

08/01/2017

• New feature to cluster genotypes and display in haplotype viewer.

03/06/2017

• RDBMS migrated to PostgreSQL in AWS-RDS
• Trait genes browser (all chromosomes viewer/ideogram)
• Four (MH63,ZS97,N22,IR8) new reference genomes/cdna/cds/pep made available for BLAST search

12/12/2016

• Query gene loci by SNP list annotates the markers and genes from various sources
• Genotype similary search with any of the varieties
• Search and highlight variety or variety list in MDS plot
• Make MDS points proportional to phenotype value
• Submit locus list/gene set to enrichment/network analysis sites

09/19/2016

• URL changed to http://snp-seek.irri.org
• HDRA varieties added with phenotype data from GRIMS
• Option to use either 3kRGP, HDRA or both datasets
• Web services documentation made public
• Alternate sequence download using GATK tool

05/16/2016

• Option to query SNP set to either (All 32M SNPs in previous version, Base 18M, Filtered 4.8M or Core 404k)
• Subpopulations renamed: trop1->trop, trop2->subtrop
• Result for SNP Effect program on MSU7 gene loci
• More SNP annotations in Locus query by SNP List (promoters, RiceNet and PRIN gene interactions)

03/23/2016

• Increase QNP query length to 5mb region, or lists with 1000 gene loci, or 500k SNP positions (not displayed but for download only)
• Query and match the 3k varieties using genotypes (SNP list with allele column)
• Matching option for missing alleles
• Long downloads are run in the background

02/04/2016

• Search genes using gene names/symbols/accessions
• Added TO/PO ontology (from Oryzabase) and QTARO trait genes annotation to SNP lists
• Gene information page and external links

12/30/2015

• New homepage icons
• Support for multiple reference genomes (Nipponbare, 9311, IR64-21, Kasalath, DJ123)
• Display alleles in all 5 reference genomes in SNP query
• Display other reference genomes and gene models in JBrowse
• Display pairwise alignments between any of the 5 reference genomes
• Variety phenotypes are mapped and can be queried by Rice Crop Ontology (C0_320) and Plant trait Ontology (TO)
• Locus query for SNP lists returns genes for 3 Nipponbare gene models, QTARO and Gramene QTLs

10/26/2015

• In addition to MSU7, gene loci now includes RAP and our merged MSU7, RAP and FGenesh++ gene models. Loci from any of the three are merged if they have >50% overlap on the CDS
• Query gene loci by Gene Ontology terms
• Query gene loci by Traits (QTARO) and Trait and Plant Ontologies (from TO, PO using Oryzabase)

09/29/2015

• Using updated SNPs/Indel data with 3024 varieties
• Updated subpopulations
• Download links for BAM and VCF from Amazon S3
• New JBrowse tracks for BAM, VCF, Trait loci, Gene models
• Option to include Indels in query
• Option to display phenotype value in genotype table
• Generate alternate sequence from the VCF files

06/02/2015

• Download links for FastQ and FastQC reports
• Allele frequency calculation on SNP Query results

05/04/2015

• SNP Query using SNP list with multiple contigs/chromosomes in a list
• SNP Query using Gene Loci list
• Transitive closure is used for Loci search by Gene Ontology term
• Added Loci search by sequence using BLAST on locus, cds, protein and 3kbp-upstream sequences for all 5 reference genomes

04/13/2015

• Allow filtering of genotype table by ALLELE value, variety and mismatch
• Allow sorting of genotype table by ALLELE value, variety and mismatch
• SNP Genotype track in JBrowse is updated after filtering and sorting operations
• Gene loci search by SNP list supports multiple contigs/chromosomes in a list

03/30/2015

• Added search Gene loci by region and SNP list
• Added search Gene loci by sequence using Blast on Nipponbare cds, cdna and proteins
• Added search Genomic region by sequence using Blast on Nipponbare, IR64-21, 9311, DJ123 and Kasalat genomes

03/12/2015

• Added search Gene loci by gene function
• Create gene locus list from Loci Search result and through My Lists editor

03/3/2015

• Added options to include, exclude or highlight non-synonymous/synonymous SNPs
• Highlight slice acceptor and splice donor SNPs
• Query length for Core SNPs limited to 1Mbp, and All SNPs to 50kbp to avoid Out of Memory Error and crashing the server

02/16/2015

• Country of origin is updated (from GRIMS passport field ori_country to country_origin)
• Added option to Include, Highlight or Exclude Synonymous SNPs
• Genotype table is revised from ZK Grid to use ZK Biglistbox for fast rendering of long regions
• Added Alignment Tab panel to display, sort, or export Genotype data as Multiple Sequence Alignments (in preparation to display Indels)