Journal Article

RadishBase: A Database for Genomics and Genetics of Radish

Di Shen, Honghe Sun, Mingyun Huang, Yi Zheng, Xixiang Li and Zhangjun Fei

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 54, issue 2, pages e3-e3
Published in print February 2013 | ISSN: 0032-0781
Published online December 2012 | e-ISSN: 1471-9053 | DOI: https://dx.doi.org/10.1093/pcp/pcs176
RadishBase: A Database for Genomics and Genetics of Radish

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry

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Radish is an economically important vegetable crop. During the past several years, large-scale genomics and genetics resources have been accumulated for this species. To store, query, analyze and integrate these radish resources efficiently, we have developed RadishBase (http://bioinfo.bti.cornell.edu/radish), a genomics and genetics database of radish. Currently the database contains radish mitochondrial genome sequences, expressed sequence tag (EST) and unigene sequences and annotations, biochemical pathways, EST-derived single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, and genetic maps. RadishBase is designed to enable users easily to retrieve and visualize biologically important information through a set of efficient query interfaces and analysis tools, including the BLAST search and unigene annotation query interfaces, and tools to classify unigenes functionally, to identify enriched gene ontology (GO) terms and to visualize genetic maps. A database containing radish pathways predicted from unigene sequences is also included in RadishBase. The tools and interfaces in RadishBase allow efficient mining of recently released and continually expanding large-scale radish genomics and genetics data sets, including the radish genome sequences and RNA-seq data sets.

Keywords: radish; genomics; genetics; database

Journal Article.  2075 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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