Reconstruction and Annotation of Transcribed Sequences in Plants

基因组学提供了一个很好的机会，以确定在不同的生物体集合的基因的整个补充，并提供了必要的工具，开始了解这些基因在发育，疾病和进化中发挥的作用。表达序列标签（EST）的测序提供了许多生物体中转录序列集合的第一印象，并且通过对EST数据的彻底分析可以获得重要的额外信息。TIGR对基因索引（http：//www.tigr.org/tdb/tdb.html）中记录的世界人类EST序列数据集的分析提供了高置信度的重复一致序列，代表了TIGR对EST基础转录序列集的最佳估计。基于为分析人类EST序列而开发的技术，TIGR维护各种重要模式生物的基因索引，包括拟南芥基因索引（AtGI）、水稻基因索引（OGI）、番茄基因索引（LGI）和马铃薯基因索引。总之，这些基因索引代表了植物基因比较分析的独特资源，并可能提供对基因功能，调控和进化的见解。最近在各种重要作物物种中的EST测序项目提供了创建其他植物物种（包括玉米（Zea mays）和大豆（Glycine max））的基因索引所需的序列数据。该项目将为这些植物创建基因索引，继续组装现有的植物基因索引，并对索引进行一些改进，包括季度发布，扩展注释，整合映射和基因组序列数据，以及更强大的搜索功能。此外，该项目将产生一套植物直系同源物，并开发一个基于网络的演示文稿，允许这些直系同源物集的属性进行探索。这样的数据库将提供植物EST组装之间的直接联系，并将代表最广泛的植物直系同源物目录，为基因鉴定、功能结构域的阐明以及基因和基因组进化的分析提供有价值的资源。

Genomics has provided a great opportunity to identify the entire complement of genes within a diverse collection of organisms and has provided the tools necessary to begin to understand the role these genes play in development, disease, and evolution. The sequencing of Expressed Sequence Tags (ESTs) has provided a firstglimpse of the collection of transcribed sequences in many organisms, and significant additional information can be obtained by a thorough analysis of the EST data. TIGR's analysis of the world's collection of human EST sequence data, captured in the Gene Indices (http://www.tigr.org/tdb/tdb.html), provides assembledconsensus sequences that are of high confidence and represent TIGR's best estimate of the collection of transcribed sequences underlying the ESTs. Based on the techniques developed for analysis of human EST sequences, TIGR maintains Gene Indices for a variety of important model organisms, including the Arabidopsis Gene Index (AtGI), the Rice Gene Index (OGI), the Tomato Gene Index (LGI) and the Potato Gene Index. Together, these Gene Indices represent a unique resource for the comparative analysis of plant genes and may provide insight into gene function, regulation, and evolution. Recent EST sequencing projects in a variety of important crop species have provided the sequence data necessary to create Gene Indices for additional plant species, including Maize (Zea mays) and Soybean (Glycine max). This project will create Gene Indices for these plants, continue to assemble the existing Plant Gene Indices, and make a number of improvements in the Indices, including quarterly releases, expanded annotation, integration with mapping and genomic sequence data, and more robust search capabilities. In addition, the project will generate a set of plant orthologues and develop a web-based presentation allowing the properties of these orthologue sets to be explored. Such a database would provide direct links between the plant EST assemblies and would represent the most extensive catalog of plant orthologues, providing a valuable resource for gene identification, elucidation of functional domains, and analysis of gene and genome evolution.