SNP-Seek


NAR Molecular Biology Database Collection entry number 1823
Alexandrov, Nickolai; Mansueto, Locedie; Palis, Kevin; Fuentes, Roven; Ulat, Victor; Chebotarov, Dmytro; Tai, Shuaishuai; Zhang, Gengyun; Li, Zhikang; Mauleon, Ramil; Hamilton, Ruaraidh; McNally, Kenneth

Database Description

The Rice SNP-Seek Database features SNP data from various cultivars alongside the Nipponbare reference genome: IR 64, 93-11, DJ 123 and Kasalath. Genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. 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.

Category: Plant databases
Subcategory: Rice

Go to the abstract in the NAR 2017 Database Issue.
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