Reconstruction and Annotation of Transcribed Sequences in Plants

PI: John Quackenbush （Dana-Farber癌症研究所）基因组计划的主要目标是在一个特定物种中识别和描述整个基因目录的功能特征。虽然基因组测序项目提供了丰富的数据，但发现和编目基因及其变异仍然是一个重大挑战。由于这个原因，除其他外，尽管基因组测序项目已经启动的物种越来越多，但来自基因转录本的表达序列标签（est）测序仍然是生物学研究的重要工具。est为测序物种的基因鉴定提供了宝贵的数据，为非编码但生物学上重要的基因组特征提供了证据，并且在许多物种中，提供了关于其基因内容的唯一可用信息。基因索引数据库（TGI; http://compbio.dfci.harvard.edu/tgi/plant.html）的开发是为了提供高质量的、公开可用的EST序列分析，目前代表了超过34种不同的植物物种。TGI提供了跨物种这些数据的一致视图。该项目将使TGI数据库中植物和植物寄生虫物种的数量增加一倍以上。这些数据库和相关的软件工具将促进广泛的植物功能基因组学研究，将有助于鉴定可用于植物育种和病原体抗性研究的基因，并将有助于在未来几年测序的植物基因组的注释。通过本提案开发的所有方法都将在免费提供的开源软件工具中实例化。这将允许其他研究人员在他们的家庭机构中忠实地复制TGI，并为开发和维护基因指数提供另一种方法。多年来，TGI项目为研究界做出了许多重要贡献，包括创建了一个高度使用和被广泛引用的公共数据库，广泛使用的软件工具来分析EST数据，以及培训了许多学生和博士后。具体来说，通过该项目创建的数据库将继续不受限制地通过http://compbio.dfci.harvard.edu/tgi/plant.html提供，网络服务的访问将允许其他工厂数据库更有效地与通过TGI提供的资源链接，预计在未来几年，这些数据库将远远超过2006年这些数据库收到的近1500万次网络点击。该项目将继续支持与各种植物基因组研究小组的合作，欢迎他们的人员作为访客，更有效地将项目间的资源联系起来，并提供关于TGI资源使用的研讨会。

PI: John Quackenbush (Dana-Farber Cancer Institute)The primary goal of a genome project is the identification and functional characterization of the entire catalog of genes within a particular species. While genome sequencing projects have provided a wealth of data, finding and cataloging genes and their variants remains a significant challenge. For this reason, among others, the sequencing of Expressed Sequence Tags (ESTs) derived from genes transcripts remains an important tool for biological inquiry despite the growing number of species for which genome sequencing projects have been initiated. ESTs provide valuable data for gene identification in sequenced species, provide evidence for non-coding but biologically important genomic features, and, in many species, provide the only information available about their gene content. The Gene Index databases (TGI; http://compbio.dfci.harvard.edu/tgi/plant.html) were developed to provide a high-quality, publicly available analysis of EST sequences and currently represent more than 34 different plant species. The TGI provide a consistent view of these data across species. This project will more than double the number of plant and plant parasite species represented in the TGI databases. The databases and the associated software tools will facilitate a wide range of plant functional genomics studies, will assist in identification of genes that can be used, for example, in plant breeding and the study of pathogen resistance, and will contribute to the annotation of plant genomes that will be sequenced in the coming years. All methods developed through this proposal will be instantiated in freely available, open source software tools. This will allow other researchers to faithfully reproduce the TGI in their home institutions and offer an alternative approach to the development and maintenance of gene indices.Broader ImpactOver the years, the TGI project has made a number of important contributions to the research community, including the creation of a highly used and well-cited public collection of databases, widely used software tools for the analysis of EST data, and the training of a number of students and postdocs. Specifically, the databases created through this project will continue to be available without restriction through http://compbio.dfci.harvard.edu/tgi/plant.html and web services access will allow other plant databases to link more effectively to the resources provided through the TGI and it is expected that in the coming years the databases will see far more than the nearly 15 million web hits these databases received in 2006. This project will continue to support collaboration with a variety of plant genome research groups, to welcome their personnel as visitors to more effectively link resources across projects, and to offer workshops on the use of the TGI resources.