GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research.
GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research.
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DOI：
10.1186/1471-2105-5-130
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发表时间：
2004-09-09
影响因子：
3
通讯作者：
Main D
中科院分区：
文献类型：
--
作者：
Jung S;Jesudurai C;Staton M;Du Z;Ficklin S;Cho I;Abbott A;Tomkins J;Main D
桃是蔷薇科的模式生物，蔷薇科是一个重要的经济科，包括水果和观赏植物，如苹果、梨、草莓、樱桃、杏仁和玫瑰。桃的基因组学和遗传学数据对近缘物种的基因发现和遗传理解具有重要意义。然而，这些桃资源的有效利用，需要开发一个集成的和集中的数据库与相关的分析工具。蔷薇科基因组数据库（GDR）是一个精心策划和集成的基于Web的关系数据库。GDR包含遗传锚定的桃物理图谱、注释的桃EST数据库、蔷薇科图谱和标记以及所有公开可用的蔷薇科序列的全面数据。EST的注释包括重叠群组装、推定功能、简单序列重复和在适用的情况下锚定到桃物理图的位置。我们的综合地图查看器提供了图形界面的遗传，转录组和物理映射信息。EST、BAC和标记可按不同类别查询，搜索结果网站链接到综合地图查看器或WebFPC物理地图网站。除了浏览和查询数据库外，用户还可以通过运行BLAST或FASTA算法的专用序列相似性服务器将其序列与注释的GDR序列进行比较。为了证明综合和充分注释的数据库和分析工具的实用性，我们描述了一个案例研究，我们锚定蔷薇科序列的桃的物理和遗传图谱的序列相似性。GDR的启动是为了解决蔷薇科基因组学和遗传学研究的主要缺陷，即集中的网络数据库和用于数据存储，分析和交换的生物信息学工具。可以访问GDR。
Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at .