SNP-Seek Database

Next-generation sequencing technologies allow us to identify variations over a large number of genomes. Using published software and computational pipelines, we identified SNP and short InDels from the 3k Rice Genomes Project. The SNP-Seek database and web application (http://oryzasnp.org/iric-portal) allow access to the results of these analyses to rice researchers and breeders worldwide. Along with the variant data we generated, SNP-Seek also provides germplasm passport and phenotypic data for the 3,000 resequenced accessions, genomic sequence and gene annotations (RAP, MSU),  ontologies (GO, PO, TO, CO),  trait genes and QTL from Oryzabase and Q-TARO. Our goal is to establish a platform integrating various biological data and sources to facilitate the discovery of new rice gene-trait associations.

Users can query for SNP and InDel genotypes constrained by variety and region, then view and manipulate the results in table or genome browser along with other genome features. Varieties query is constrained by passport or phenotype values, through an interactive tree viewer or an MDS plot showing the phylogenetic distances between all the varieties.  Gene loci are queried constrained by region, SNP positions or ontologies exploiting transitive closure. We also implemented a List Manager, serving the role of a 'shopping cart' of data, which handles lists of SNP positions, Varieties and Loci. These lists are generated from query results or created in an editor, and may be used as constraint to queries, or downloaded for future reference. A web-service API is also available to query SNP-Seek programmatically.