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Nucleic Acids Res. 2017 Jan 4;45(D1):D1075-D1081. doi: 10.1093/nar/gkw1135. Epub 2016 Nov 29.

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

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International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
Boyce Thompson Institute, Ithaca, NY 14853, USA.
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85750, USA.
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
Softberry, Inc., Mount Kisco, NY 10549, USA.
International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines


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. 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:

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