HIGH THROUGHPUT ANNOTATION OF GENOMIC DNA SEQUENCE

描述(申请人摘要)：现在， 人类基因组已在手中，正在进行的努力正在到位，以提供 小鼠基因组，挑战是识别由这些基因编码的基因 基因组。在这方面正在进行几项努力，包括我们自己使用ab 以mRNAs和EST形式的初始基因发现者和转录序列。 基因预测是识别基因的第一步。其他步骤包括 预测这些基因的功能并关联任何其他信息，如 基因可能在哪里(以及何时)表达。拟议项目的目标是 是提供一个公共数据库，它将提供一个基因的中央储存库 预测和关联的注释。该项目将提供数据 整合使得对同一基因的预测和注释(如定义的 通过共同定位到相同的基因组位置)将被链接。关联的 将扩展注释以包括函数预测和表达式 配置文件。该数据库的预期用户是寻求扩展的研究人员 他们对一个基因的了解始于一个表达谱、一个cDNA或一个 基因座或一般搜索候选基因。原型机 基因组序列的注释框架Gaia已经与 ESTs和mRNAs、DOTS和基因整合的基因索引的原型， EpoDB。结果是一个基于全局模式GUS的数据库，它集成了 来自GenBank、DBEST和Swiss-prot的以序列为中心的条目和转换 进入以基因为中心的实体的条目。此过程包括数据清理 以及通过注释合成的基因(mRNAs和 蛋白质)。该资源的第一次传递是通过即席布尔查询在线的 和集成的可视化工具，如www.allgenes.org。该资源将提供 来自GenBank的已知和预测基因的集成集、基因查找器和 组装的ESTs和mRNA.将使用本体来构建注释的结构 生物学概念和基因功能。基因表达信息将被 增加了RAD(RNA丰度数据库)。没有这方面的其他公共资源 自然目前是存在的。将维护该资源的数据通用性 通过每2-3个月定期更新。更新将包括集成 包含新可用的GenBank和DBEST条目的先前注释的基因 并重新计算基因相似性、基因位置、组织分布和 基因的功能。开发了一个注释接口，以补充和 通过手动评估以下项目的预测来扩展计算分析 基因及其功能。用于鼠标序列的辐射杂交映射数据 将被合并，就像人类EST所做的那样。基因之间的联系 在GUS中，将建立RAD中的基因表达数据。以回应 公共社区，对Web界面的查询将合并并批量进行 为回应allgenes.org网站用户而提供的文件。计划中的是 包括新重叠群的按需注释。

DESCRIPTION (Applicant's abstract): Now that a working draft sequence of the human genome is in hand and an ongoing effort is in place to provide a draft of the mouse genome, the challenge is to identify the genes encoded by these genomes. Several efforts are underway in this regard including our own using ab initio gene finders and transcribed sequences in the form of mRNAs and ESTs. Gene prediction is the first step in identifying genes. Additional steps are to predict the function of those genes and associate any other information such as where (and when) the gene might be expressed. The goal of the proposed project is to provide a public database that will provide a central repository of gene predictions and associated annotation. The project will provide data integration such that predictions and annotations for the same gene (as defined by co-localizing to the same genomic location) will be linked. Associated annotation will be extended to include functional predictions and expression profiles. The intended users of the database are researchers seeking to extend their knowledge of a gene starting with an expression profile, a cDNA, or a genetic locus or to search generally for candidates genes. The prototype annotation framework for genomic sequence, GAIA, has been combined with prototypes for a gene index of ESTs and mRNAs, DoTS, and gene integration, EpoDB. The result is a database based on a global schema, GUS, that integrates sequence-centered entries from GenBank, dbEST, and SWISS-PROT and transforms the entries into gene-centered entities. This process includes data cleansing and adding value through annotation of the resultant genes (mRNAs and proteins). A first pass of this resource is on-line with ad hoc boolean queries and integrated visual tools as www.allgenes.org. The resource will provide an integrated set of known and predicted genes from GenBank, gene finders, and assembled ESTs and mRNA. Ontologies will be used to structure the annotations of biological concepts and gene function. Gene expression information will be augmented with RAD (RNA Abundance Database). No other public resource of this nature currently exists. Data currency of this resource will be maintained through periodic updates every 2-3 months. The updates will include integration of previously annotated genes with newly available GenBank and dbEST entries and recalculation of gene similarities, gene location, tissue distribution, and gene function. An annotation interface has been developed to complement and extend computational analysis through manual assessment of predictions for genes and their functions. Radiation hybrid mapping data for mouse sequences will be incorporated as has been done for human ESTs. Links between the genes in GUS and gene expression data in RAD will be established. To respond to the public community, queries to the web interface will be incorporated and bulk files provided in response to users of the allgenes.org site. Planned is the inclusion of on-demand annotation of new contigs.