Databases and information integration for the Medicago truncatula genome and transcriptome
Databases and information integration for the Medicago truncatula genome and transcriptome
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DOI：
10.1104/pp.104.059204
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发表时间：
2005-05-01
期刊：
影响因子：
7.4
通讯作者：
Retzel, EF
中科院分区：
文献类型：
--
作者：
Cannon, SB;Crow, JA;Retzel, EF
一个国际联盟正在对苜蓿的常染色质基因空间进行测序。广泛的生物信息学和数据库资源支持标记锚定细菌人工染色体（BAC）测序策略。现有的物理和遗传图谱以及深BAC端测序有助于指导测序工作，而EST数据库为基因组注释、转录组表征和微阵列设计提供了必要的资源。完成的BAC序列被连接到重叠的序列组装中，并经历一个自动化的注释过程，该过程集成了从头算预测与EST、蛋白质和其他可识别的特征。由于测序项目的国际性和合作性，数据生产、存储和可视化工具广泛分布。本文描述了该项目的数据库和Web资源，为物理和遗传图谱、基因组序列组装、基因预测和EST数据集成提供了支持。medicago的一个中心项目网站。org/ genome提供了对基因组查看器和其他项目范围内资源的访问，包括在medicago的Ensembl实现。Org， mtgenome的物理地图和标记资源。ucdavis。edu，以及俄克拉荷马大学（University of Oklahoma）的基因组观察者。基因组。ou。edu)，基因组研究所(www。tigr。org)和慕尼黑蛋白质序列信息中心（mips. org）。确定。德)。
An international consortium is sequencing the euchromatic genespace of Medicago truncatula. Extensive bioinformatic and database resources support the marker- anchored bacterial artificial chromosome ( BAC) sequencing strategy. Existing physical and genetic maps and deep BAC- end sequencing help to guide the sequencing effort, while EST databases provide essential resources for genome annotation as well as transcriptome characterization and microarray design. Finished BAC sequences are joined into overlapping sequence assemblies and undergo an automated annotation process that integrates ab initio predictions with EST, protein, and other recognizable features. Because of the sequencing project's international and collaborative nature, data production, storage, and visualization tools are broadly distributed. This paper describes databases and Web resources for the project, which provide support for physical and genetic maps, genome sequence assembly, gene prediction, and integration of EST data. A central project Web site at medicago. org/ genome provides access to genome viewers and other resources project- wide, including an Ensembl implementation at medicago. org, physical map and marker resources at mtgenome. ucdavis. edu, and genome viewers at the University of Oklahoma ( www. genome. ou. edu), the Institute for Genomic Research ( www. tigr. org), and Munich Information for Protein Sequences Center ( mips. gsf. de).