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RadishBase: A Database for Genomics and Genetics of Radish

文献类型： 外文期刊

作者： Shen, Di 1 ; Sun, Honghe 2 ; Huang, Mingyun 2 ; Zheng, Yi 2 ; Li, Xixiang 1 ; Fei, Zhangjun 2 ;

作者机构： 1.Chinese Acad Agr Sci, Key Lab Hort Crop Biol & Germplasm Innovat, Minist Agr, Inst Vegetables & Flowers, Beijing 100081, Peoples R China

2.Cornell Univ, Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA

3.Beijing Acad Agr & Forestry Sci, Natl Engn Res Ctr Vegetables, Beijing 100097, Peoples R China

4.USDA ARS, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA

关键词： radish;genomics;genetics;database

期刊名称：PLANT AND CELL PHYSIOLOGY （ 影响因子：4.927； 五年影响因子：5.516 ）

ISSN： 0032-0781

年卷期： 2013 年 54 卷 2 期

页码：

收录情况： SCI

摘要： 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 ( ext-link-type="uri" xlink:href="http://bioinfo.bti.cornell.edu/radish" xmlns:xlink="http://www.w3.org/1999/xlink">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.

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