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Rice SNP-seek database update: new SNPs, indels, and queries
Locedie Mansueto1, Roven Rommel Fuentes1, Frances Nikki Borja1
1International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
Nucleic Acids Research
|December 1, 2016
Summary
The updated Rice SNP-Seek Database offers enhanced querying of single nucleotide polymorphism (SNP) datasets across multiple rice genomes. This resource facilitates streamlined gene-trait association discovery for researchers.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- The Rice SNP-Seek Database provides a valuable resource for exploring genetic variation in rice.
- Previous versions required updates to accommodate new data and improve user accessibility.
Purpose of the Study:
- To describe significant updates and new features implemented in the Rice SNP-Seek Database.
- To enhance data accessibility, querying capabilities, and analytical functions for rice genetic research.
Main Methods:
- A new SNP-calling pipeline and filtering process were employed to generate comprehensive SNP datasets.
- The pipeline was applied to multiple rice genome assemblies, including Nipponbare, IR 64, 93-11, DJ 123, and Kasalath.
- JBrowse was integrated for visualization of various annotation tracks and genome comparison, alongside middleware redesign for performance optimization.
Main Results:
- Complete, base, filtered, and core SNP datasets were generated for multiple rice varieties.
- New genotype query and display features, along with an integrated list manager and SNP Annotator, were implemented.
- Web-service access was established for most data, enabling seamless querying across biological entities.
Conclusions:
- The updated Rice SNP-Seek Database offers significantly improved functionality for querying and analyzing rice genetic data.
- These enhancements represent a significant step towards semi-automated gene-trait association discovery in rice.
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