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

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dc.creatorMansueto, Locedie
dc.creatorFuentes, Roven Rommel
dc.creatorBorja, Frances Nikki
dc.creatorDetras, Jeffery
dc.creatorAbriol-Santos, Juan Miguel
dc.creatorChebotarov, Dmytro
dc.creatorSanciangco, Millicent
dc.creatorPalis, Kevin
dc.creatorCopetti, Dario
dc.creatorPoliakov, Alexandre
dc.creatorDubchak, Inna
dc.creatorSolovyev, Victor
dc.creatorWing, Rod A.
dc.creatorHamilton, Ruaraidh Sackville
dc.creatorMauleon, Ramil
dc.creatorMcNally, Kenneth L.
dc.creatorAlexandrov, Nickolai
dc.date2017-01-04
dc.date2024-12-19T12:54:46Z
dc.date2024-12-19T12:54:46Z
dc.date.accessioned2026-06-27T04:14:15Z
dc.descriptionWe 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. 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
dc.identifierhttps://hdl.handle.net/10568/165174
dc.identifier.urihttp://hdl.handle.net/123456789/26112
dc.languageen
dc.publisherOxford University Press
dc.rightsOpen Access
dc.sourceMansueto, Locedie; Fuentes, Roven Rommel; Borja, Frances Nikki; Detras, Jeffery; Abriol-Santos, Juan Miguel; Chebotarov, Dmytro; Sanciangco, Millicent; Palis, Kevin; Copetti, Dario; Poliakov, Alexandre; Dubchak, Inna; Solovyev, Victor; Wing, Rod A.; Hamilton, Ruaraidh Sackville; Mauleon, Ramil; McNally, Kenneth L. and Alexandrov, Nickolai. 2017. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res, Volume 45 no. D1 p. D1075-D1081
dc.titleRice SNP-seek database update: new SNPs, indels, and queries
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)