Rice SNP-seek database update: New SNPs, indels, and queries

Locedie Mansueto, Roven Rommel Fuentes, Frances Nikki Borja, Jeffery Detras, Juan Miguel Abrio-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

Research output: Contribution to journalArticlepeer-review

73 Scopus citations

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. Webservice calls were implemented to access most data. These features enable seamless querying of SNPSeek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.

Original languageEnglish (US)
Pages (from-to)D1075-D1081
JournalNucleic acids research
Volume45
Issue numberD1
DOIs
StatePublished - Jan 1 2017

ASJC Scopus subject areas

  • Genetics

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