Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
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DOI：
10.1186/1741-7007-3-7
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发表时间：
2005-03-22
期刊：
影响因子：
5.4
通讯作者：
Town CD
中科院分区：
文献类型：
--
作者：
Haas BJ;Wortman JR;Ronning CM;Hannick LI;Smith RK Jr;Maiti R;Chan AP;Yu C;Farzad M;Wu D;White O;Town CD
自从首次公布其完整的基因组序列以来，拟南芥作为植物研究的模型变得比以往任何时候都重要。然而，最初的基因组注释是由多个中心使用不一致的方法提交的，这使得数据难以用于许多应用。在三年的时间里，TIGR已经完成了对拟南芥基因组结构和功能注释的标准化工作。使用手动和自动化的方法，拟南芥基因结构的精炼和基因产物被重命名，并分配到基因本体论类别。我们概述了所采用的方法，开发的工具和遵循的协议，总结了每个数据发布的内容，特别强调我们的最终注释发布（版本5）。在整个时期内，数千个新基因和假基因被添加到注释中。大约三分之一的原始注释的基因模型显着细化产生改进的基因结构注释，每个蛋白质编码基因进行手动检查和分类使用基因本体论术语。
Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications. Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5). Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.
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